installing on windows 10

[neurostm]

Hello,
I am having some issues installing the software on a new computer. I have done everything the same way as I did while installing the software on an older laptop.
I get the following output from R:

Downloading GitHub repo tractatus/wholebrain@master
     
   checking for file 'C:\Users\Rotenberg-admin\AppData\Local\Temp\RtmpQVKVBX\remotes3b44bee4\tractatus-wholebrain-8e12757/DESCRIPTION' ...
  
√  checking for file 'C:\Users\Rotenberg-admin\AppData\Local\Temp\RtmpQVKVBX\remotes3b44bee4\tractatus-wholebrain-8e12757/DESCRIPTION'

  
  
  
-  preparing 'wholebrain': (2.6s)
   checking DESCRIPTION meta-information ...
  
√  checking DESCRIPTION meta-information
-  cleaning src

  
  
  
-  checking for LF line-endings in source and make files and shell scripts

  
  
  
-  checking for empty or unneeded directories (1.2s)

  
  
  
-  looking to see if a 'data/datalist' file should be added

  
  
  
-  building 'wholebrain_0.1.1.tar.gz' (2s)

  
   

* installing *source* package 'wholebrain' ...
** using staged installation
** libs
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c CThinPlateSpline.cpp -o CThinPlateSpline.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c CoherentPointShift.cpp -o CoherentPointShift.o
CoherentPointShift.cpp: In function 'SEXPREC* CoherentPointDriftRegistration(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
CoherentPointShift.cpp:24:12: warning: unused variable 'beta' [-Wunused-variable]
     double beta = Rcpp::as<double>(betaR);
            ^
CoherentPointShift.cpp:25:12: warning: unused variable 'lambda' [-Wunused-variable]
     double lambda = Rcpp::as<double>(lambdaR);
            ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c DoubleSlider.cpp -o DoubleSlider.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c ThinPlateSpline.cpp -o ThinPlateSpline.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c Widget.cpp -o Widget.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c affine.cpp -o affine.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c connectedcomponents3D.cpp -o connectedcomponents3D.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c display.cpp -o display.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c filter.cpp -o filter.o
filter.cpp: In function 'void FindBlobs(const cv::Mat&, std::vector<std::vector<cv::Point_<int> > >&, int)':
filter.cpp:142:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(blob.size()>lengthlimitation){
                           ^
filter.cpp: In function 'void stepwisethreshold(const cv::Mat&, std::vector<int>, bool, double, double, std::vector<std::vector<cv::Point_<int> > >&, std::vector<cv::Vec<int, 4> >&, cv::Mat&)':
filter.cpp:317:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i = 0; i< contours.size(); i++ ){
                      ^
filter.cpp: In member function 'void StepThreshold::runthreshold()':
filter.cpp:383:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int j=0; j<numThresholds; j++){
                               ^
filter.cpp:388:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<numThresholds; i++) {
                               ^
filter.cpp:452:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< contours.size(); i++ ){
                          ^
filter.cpp:461:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< contours.size(); i++ ){
                          ^
filter.cpp:476:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< contours.size(); i++ ){
                          ^
filter.cpp: In function 'void copySourceTile(const cv::Mat&, cv::Mat&, cv::Rect&)':
filter.cpp:676:10: warning: variable 'tl' set but not used [-Wunused-but-set-variable]
     auto tl = tile.tl();
          ^
filter.cpp: In function 'SEXPREC* getContours(SEXP, SEXP, SEXP)':
filter.cpp:928:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i = 0; i< contours.size(); i++ )
                      ^
filter.cpp: In function 'SEXPREC* filterImage(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
filter.cpp:1062:9: warning: unused variable 'oldRowW' [-Wunused-variable]
     int oldRowW = rowsW;
         ^
filter.cpp:1065:10: warning: variable 'oldsize' set but not used [-Wunused-but-set-variable]
     Size oldsize = tobefiltered.size();
          ^
filter.cpp:1002:7: warning: unused variable 'nofilter' [-Wunused-variable]
   int nofilter = Rcpp::as<int>(noFilter); //change to bool
       ^
filter.cpp:1003:7: warning: unused variable 'filterminArea' [-Wunused-variable]
   int filterminArea = Rcpp::as<int>(filter_minArea);
       ^
filter.cpp:1004:7: warning: unused variable 'filtermaxArea' [-Wunused-variable]
   int filtermaxArea = Rcpp::as<int>(filter_maxArea);
       ^
filter.cpp:1005:7: warning: unused variable 'filterminThresh' [-Wunused-variable]
   int filterminThresh = Rcpp::as<int>(filter_minThresh);
       ^
filter.cpp:1006:7: warning: unused variable 'filtermaxThresh' [-Wunused-variable]
   int filtermaxThresh = Rcpp::as<int>(filter_maxThresh);
       ^
filter.cpp:1007:7: warning: unused variable 'filtereccentricity' [-Wunused-variable]
   int filtereccentricity = Rcpp::as<int>(filter_eccentricity);
       ^
In file included from C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/core.hpp:58:0,
                 from C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/opencv.hpp:52,
                 from filter.cpp:2:
C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/core/types.hpp: In function 'SEXPREC* createTiles(SEXP, SEXP, SEXP, SEXP, SEXP)':
C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/core/types.hpp:1828:50: warning: 'y0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     : x(_x), y(_y), width(_width), height(_height) {}
                                                  ^
filter.cpp:796:9: note: 'y0' was declared here
     int y0;
         ^
In file included from C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/core.hpp:58:0,
                 from C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/opencv.hpp:52,
                 from filter.cpp:2:
C:\WHOLEB~1\R\R361\library\opencv\include/opencv2/core/types.hpp:1828:50: warning: 'x0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     : x(_x), y(_y), width(_width), height(_height) {}
                                                  ^
filter.cpp:795:9: note: 'x0' was declared here
     int x0;
         ^
filter.cpp:793:16: warning: 'newWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     finalImage = Mat::zeros(newHeight, newWidth, sourceImage.type());
                ^
filter.cpp:793:16: warning: 'newHeight' may be used uninitialized in this function [-Wmaybe-uninitialized]
filter.cpp: In function 'SEXPREC* interactiveThreshold(SEXP, SEXP)':
filter.cpp:605:55: warning: 'depth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     pd.src.convertTo(srcFloat,CV_32F,255/(double)depth);
                                                       ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c flatfieldcorrection.cpp -o flatfieldcorrection.o
flatfieldcorrection.cpp: In function 'void getGain(int, int, int, std::vector<cv::Mat>&, cv::Mat&, bool)':
flatfieldcorrection.cpp:64:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(size_t s = 0; s != STACKS; ++s){
                               ^
flatfieldcorrection.cpp:45:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
flatfieldcorrection.cpp: In function 'SEXPREC* posteriorFFC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
flatfieldcorrection.cpp:170:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(size_t s = 0; s != num_files; ++s){
                      ^
flatfieldcorrection.cpp:108:7: warning: unused variable 'DISPLAY' [-Wunused-variable]
   int DISPLAY = Rcpp::as<int>(display);
       ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c gauss_transform.cpp -o gauss_transform.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c gauss_transform_make_default.cpp -o gauss_transform_make_default.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c getContour.cpp -o getContour.o
getContour.cpp: In function 'SEXPREC* getContour(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getContour.cpp:145:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( int i = 0; i < contours.size(); i++ )
                     ^
getContour.cpp:150:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( int i = 0; i < contours.size(); i++ )
                     ^
getContour.cpp:155:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( int i = 0; i< contours.size(); i++ )
                    ^
getContour.cpp:174:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( int i = 0; i< contours.size(); i++ )
                    ^
getContour.cpp:191:103: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<std::vector<cv::Point_<int> > >::size_type {aka long long unsigned int}' [-Wformat=]
       printf("Largest contour: %d, # contours detected: %d \n", largest_contour_index, contours.size());
                                                                                                       ^
getContour.cpp:203:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int i = 0; i< contours.size(); i++ ){
                     ^
getContour.cpp:210:48: warning: format '%d' expects argument of type 'int', but argument 2 has type 'std::vector<std::vector<cv::Point_<int> > >::size_type {aka long long unsigned int}' [-Wformat=]
     printf("LOOP DONE: %d \n", contours.size() ); 
                                                ^
getContour.cpp:238:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int j = 0; j < contours[*it].size(); ++j){
                      ^
getContour.cpp:251:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j = 0; j < contours[0].size(); ++j){
                         ^
getContour.cpp: In function 'SEXPREC* nuclearSegment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getContour.cpp:694:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i< contours.size(); ++i){
                   ^
getContour.cpp:695:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int j = 0; j < contours[i].size(); ++j){
                      ^
getContour.cpp:714:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i< contours.size(); ++i){
                    ^
getContour.cpp:715:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int j = 0; j < contours[i].size(); ++j){
                      ^
getContour.cpp:363:7: warning: unused variable 'numNested' [-Wunused-variable]
   int numNested = Rcpp::as<int>(getNested);
       ^
getContour.cpp:728:5: warning: unused variable 'numOfSegments2' [-Wunused-variable]
 int numOfSegments2 = contoursDist.size();
     ^
getContour.cpp:472:71: warning: 'depth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     threshold(img, img_bw, 0, depth, CV_THRESH_BINARY | CV_THRESH_OTSU);
                                                                       ^
getContour.cpp: In function 'SEXPREC* getContour(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getContour.cpp:123:59: warning: 'depth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     threshold(img, img_bw, thresh, depth, CV_THRESH_BINARY);
                                                           ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c imageconverter.cpp -o imageconverter.o
imageconverter.cpp: In function 'SEXPREC* morphologyEx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
imageconverter.cpp:179:7: warning: unused variable 'morph_elem' [-Wunused-variable]
   int morph_elem = Rcpp::as<int>(morphElem);// 0;
       ^
imageconverter.cpp:182:13: warning: unused variable 'max_operator' [-Wunused-variable]
   int const max_operator = 4;
             ^
imageconverter.cpp:183:13: warning: unused variable 'max_elem' [-Wunused-variable]
   int const max_elem = 2;
             ^
imageconverter.cpp:184:13: warning: unused variable 'max_kernel_size' [-Wunused-variable]
   int const max_kernel_size = 21; //"Kernel size:\n 2n +1"
             ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c laplacianpyramidblending.cpp -o laplacianpyramidblending.o
laplacianpyramidblending.cpp: In member function 'void LaplacianBlending::buildGaussianPyramid()':
laplacianpyramidblending.cpp:42:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (leftLapPyr.size() > l) {
                                   ^
laplacianpyramidblending.cpp: In function 'void placeCenterTiles(int, int, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, std::vector<cv::Mat>&, cv::Mat&, bool)':
laplacianpyramidblending.cpp:225:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(size_t s = 0; s != STACKS; ++s){
                               ^
laplacianpyramidblending.cpp: In function 'void placeHorizontalOverlap(int, int, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, std::vector<cv::Mat>&, cv::Mat&, bool)':
laplacianpyramidblending.cpp:327:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(size_t s = 0; s < STACKS; ++s){
                               ^
laplacianpyramidblending.cpp: In function 'void placeVerticalOverlap(int, int, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, std::vector<cv::Mat>&, cv::Mat&, bool)':
laplacianpyramidblending.cpp:419:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(size_t s = 0; s < STACKS; ++s){
                               ^
laplacianpyramidblending.cpp: In function 'void placeSmallOverlap(int, int, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, std::vector<cv::Mat>&, cv::Mat&, bool)':
laplacianpyramidblending.cpp:505:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(size_t s = 0; s < STACKS; ++s){
                               ^
laplacianpyramidblending.cpp: In function 'SEXPREC* LaplacianBlendPipe(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplacianpyramidblending.cpp:559:7: warning: unused variable 'verticaltiles' [-Wunused-variable]
   int verticaltiles = Rcpp::as<int>(nrows);
       ^
laplacianpyramidblending.cpp:560:7: warning: unused variable 'horizontaltiles' [-Wunused-variable]
   int horizontaltiles = Rcpp::as<int>(ncols);
       ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c lwtimagetest.cpp -o lwtimagetest.o
In file included from lift.h:34:0,
                 from lwave.h:35,
                 from lwtimagetest.cpp:18:
Laurent.h: In instantiation of 'Laurent<T>::Laurent() [with T = double]':
lift.h:703:20:   required from here
Laurent.h:45:6: warning: unused variable 'degree' [-Wunused-variable]
  int degree=0;
      ^
Laurent.h:47:6: warning: unused variable 'highest' [-Wunused-variable]
  int highest = 0;
      ^
In file included from lwtimagetest.cpp:18:0:
lwave.h: In constructor 'lwt2<T>::lwt2(std::vector<_RealType>&, int, int, liftscheme&) [with T = double]':
lwave.h:372:7: warning: 'rows_ll' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int rows_ll,cols_ll,rows_lh,cols_lh;
       ^
lwave.h:372:23: warning: 'rows_lh' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int rows_ll,cols_ll,rows_lh,cols_lh;
                       ^
lwave.h:399:23: warning: 'rows_hh' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int rows_hl,cols_hl,rows_hh,cols_hh;
                       ^
lwave.h:399:7: warning: 'rows_hl' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int rows_hl,cols_hl,rows_hh,cols_hh;
       ^
In file included from lwave.h:36:0,
                 from lwtimagetest.cpp:18:
alg.h:78:3: warning: 'cols_H' may be used uninitialized in this function [-Wmaybe-uninitialized]
   for (int j=0; j < rows; j++) {
   ^
In file included from lwtimagetest.cpp:18:0:
lwave.h:351:28: note: 'cols_H' was declared here
   int rows_L,cols_L,rows_H,cols_H;
                            ^
In file included from lwave.h:36:0,
                 from lwtimagetest.cpp:18:
alg.h:78:3: warning: 'cols_L' may be used uninitialized in this function [-Wmaybe-uninitialized]
   for (int j=0; j < rows; j++) {
   ^
In file included from lwtimagetest.cpp:18:0:
lwave.h:351:14: note: 'cols_L' was declared here
   int rows_L,cols_L,rows_H,cols_H;
              ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c makeAtlasNissl.cpp -o makeAtlasNissl.o
makeAtlasNissl.cpp: In function 'SEXPREC* getAtlasNissl(SEXP, SEXP)':
makeAtlasNissl.cpp:61:10: warning: unused variable 'resizeParam' [-Wunused-variable]
   double resizeParam = (double)(7900/395);
          ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c manualsegmentation.cpp -o manualsegmentation.o
manualsegmentation.cpp: In member function 'void Segmentation::runthreshold()':
manualsegmentation.cpp:219:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0; i < brainContours.size(); i++ ){ 
                         ^
manualsegmentation.cpp:225:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0; i < brainContours.size(); i++ )
                         ^
manualsegmentation.cpp:236:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0; i< brainContours.size(); i++ )
                        ^
manualsegmentation.cpp:254:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< brainContours.size(); i++ ){
                          ^
manualsegmentation.cpp:287:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int j=0; j<numThresholds; j++){
                               ^
manualsegmentation.cpp:292:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<numThresholds; i++) {
                               ^
manualsegmentation.cpp:356:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int j = 0; j < contours[k].size(); ++j){
                                   ^
manualsegmentation.cpp:388:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< contours.size(); i++ ){
                          ^
manualsegmentation.cpp:401:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< contours.size(); i++ ){
                          ^
manualsegmentation.cpp:417:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int i = 0; i< contours.size(); i++ ){
                          ^
manualsegmentation.cpp: In function 'SEXPREC* imageshow(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
manualsegmentation.cpp:848:7: warning: variable 'depth' set but not used [-Wunused-but-set-variable]
   int depth;
       ^
manualsegmentation.cpp: In function 'SEXPREC* GUI(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
manualsegmentation.cpp:1189:24: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(channelOfInterest != 0 & pd.src.type()!=16 ){
                        ^
manualsegmentation.cpp:1281:55: warning: 'depth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     pd.src.convertTo(srcFloat,CV_32F,255/(double)depth);
                                                       ^
manualsegmentation.cpp: In function 'SEXPREC* imageshow(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
manualsegmentation.cpp:909:50: warning: array subscript is above array bounds [-Warray-bounds]
     intensitySliderImage.maxValue = rangeValues[6];
                                                  ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c matrix.cpp -o matrix.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c multiresolutiondecomposition.cpp -o multiresolutiondecomposition.o
multiresolutiondecomposition.cpp: In function 'SEXPREC* multiresolutiondecomposition(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
multiresolutiondecomposition.cpp:165:9: warning: unused variable 'oldRowW' [-Wunused-variable]
     int oldRowW = rowsW;
         ^
multiresolutiondecomposition.cpp:168:10: warning: variable 'oldsize' set but not used [-Wunused-but-set-variable]
     Size oldsize = tobefiltered.size();
          ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c nonrigid.cpp -o nonrigid.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c normalization.cpp -o normalization.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c rigid.cpp -o rigid.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c transform.cpp -o transform.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c wavelet2d.cpp -o wavelet2d.o
C:/WHOLEB~1/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/WHOLEB~1/R/R361/include" -DNDEBUG -I"C:\WHOLEB~1\R\R361\library\opencv\include\opencv2" -I"C:\WHOLEB~1\R\R361\library\opencv\include" -I"C:\WHOLEB~1\R\R361\library\opencv\x64\mingw\bin" -I"C:\FFTW/" -I../inst/include -I"C:/WholeBrain/R/R361/library/Rcpp/include"     -IC:/WholeBrain/R/R361/library/Rcpp/include   -O2 -Wall  -mtune=generic -c webfiles.cpp -o webfiles.o
webfiles.cpp: In function 'void copySrcTile(const cv::Mat&, cv::Mat&, cv::Rect&)':
webfiles.cpp:19:10: warning: variable 'tl' set but not used [-Wunused-but-set-variable]
     auto tl = tile.tl();
          ^
C:/WHOLEB~1/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o wholebrain.dll tmp.def CThinPlateSpline.o CoherentPointShift.o DoubleSlider.o ThinPlateSpline.o Widget.o affine.o connectedcomponents3D.o display.o filter.o flatfieldcorrection.o gauss_transform.o gauss_transform_make_default.o getContour.o imageconverter.o laplacianpyramidblending.o lwtimagetest.o makeAtlasNissl.o manualsegmentation.o matrix.o multiresolutiondecomposition.o nonrigid.o normalization.o rigid.o transform.o utils.o wavelet2d.o webfiles.o -LC:\WHOLEB~1\R\R361\library\opencv\x64\mingw\lib -lopencv_calib3d410 -lopencv_core410 -lopencv_features2d410 -lopencv_flann410 -lopencv_gapi410 -lopencv_highgui410 -lopencv_imgcodecs410 -lopencv_imgproc410 -lopencv_ml410 -lopencv_objdetect410 -lopencv_photo410 -lopencv_stitching410 -lopencv_video410 -lopencv_videoio410 -LC:\FFTW/ -lfftw3-3 -L..inst/include/x64 -LC:/WHOLEB~1/R/R361/bin/x64 -lR
installing to C:/WholeBrain/R/R361/library/00LOCK-wholebrain/00new/wholebrain/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'wholebrain'
    finding HTML links ... done
    add.group                               html  
    cortical.plot                           html  
    cortical.sideview                       html  
    cortical.topview                        html  
    data.summary                            html  
    find.dim                                html  
    flat.field.correction                   html  
    get.atlas.image                         html  
    get.contour                             html  
    get.cortex.layer                        html  
    get.grid.coordinates                    html  
    get.images                              html  
    get.pixel.intensity                     html  
    get.region.volume                       html  
    makewebmap                              html  
    normalize.volume                        html  
    nuclear.segment                         html  
    prune.spots                             html  
    reflect.cells                           html  
    registration                            html  
    remove.spot.outliers                    html  
    rgb2gray                                html  
    roi.cell.count                          html  
    segment                                 html  
    stitch                                  html  
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'wholebrain' in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object 'C:/WholeBrain/R/R361/library/00LOCK-wholebrain/00new/wholebrain/libs/x64/wholebrain.dll':
  LoadLibrary failure:  The specified module could not be found.

Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/WholeBrain/R/R361/library/wholebrain'
Error: Failed to install 'wholebrain' from GitHub:
  (converted from warning) installation of package ‘C:/Users/ROTENB~1/AppData/Local/Temp/RtmpQVKVBX/file3b436454275/wholebrain_0.1.1.tar.gz’ had non-zero exit status
>

Any suggestions?

Thank you!

[tractatus]

@neurostm you have a space in your Windows user name. Cant see what it is but ROTENB~1 indicates a space somewhere as well as WHOLEB~1. You cant have spaces in folder paths because Rtools provides Linux tools for installing R packages and WIndows and Linux handles spaces very differently. Change username and folders with "_" instead of space and reboot.

[tractatus]

@neurostm can see that it looks like you have a dash in the username and not a space which should be allowed. So something else why it cant link to OpenCV.

You could check if adding:

C:/WholeBrain/R/R361/library/

To PATH and restart Windows would enable R to find the compiled opencv .dlls.

[neurostm]

thank you. I installed ROpenCVLite instead of OpenCV (my computer repeatedly gave errors when I tried to install OpenCV).
Do you think that is the reason?

[tractatus]

You probably want to make sure you dont have multiple conflicting copies of OpenCV on your system. The error you are getting is essentially telling you it can compile the code but then R doesn't find the .dll to link to when running the package.

Usually what one would do is let R not remove the failed installation and check what exactly wholebrain.dll has problem linking to:

LoadLibrary failure:  The specified module could not be found.

But it involves a little bit more work:
https://stackoverflow.com/questions/7378959/how-to-check-for-dll-dependency

So usually just easier to have an educated guess. I would think it is OpenCV. So check in R:

ROpenCVLite::installOpenCV()

That opencv is installed by ROpenCVLite. If yes then it most likely is that you might need to ad the path to where ROpenCVLite installs dlls for opencv:

C:/WholeBrain/R/R361/library/

[neurostm]

Thank you for the tips! I’ll try them later this week - as for now I just gave up on windows and installed in Ubuntu!

[velonica0]

Thank you for the tips! I’ll try them later this week - as for now I just gave up on windows and installed in Ubuntu!

Have you tried it again? I'm having the same problem as you on my Windows system.