can not finish install in Windows 10

[Biglazyant]

Hello Sir,
Thank you very much for your work. I 'm very interested in implementing your project. I followed your instructions in the website, and it seems I have no problems until the last step to install wholebrain. Can you give some instructions? Thanks you very much!

devtools::install_github("tractatus/wholebrain", args='--no-multiarch')
Downloading GitHub repo tractatus/wholebrain@HEAD
√ checking for file 'C:\temp\RtmpaYD1DI\remotes3af851576f3e\tractatus-wholebrain-b9778a2/DESCRIPTION' (521ms)

• preparing 'wholebrain': (10.2s)
  √ checking DESCRIPTION meta-information ...
• cleaning src
• checking for LF line-endings in source and make files and shell scripts (653ms)
• checking for empty or unneeded directories (2.3s)
• looking to see if a 'data/datalist' file should be added (403ms)
• building 'wholebrain_0.1.1.tar.gz' (4.6s)

• installing source package 'wholebrain' ...
  ** using staged installation
  ** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c CThinPlateSpline.cpp -o CThinPlateSpline.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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(betaR);
^
CoherentPointShift.cpp:25:12: warning: unused variable 'lambda' [-Wunused-variable]
double lambda = Rcpp::as(lambdaR);
^
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c DoubleSlider.cpp -o DoubleSlider.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c ThinPlateSpline.cpp -o ThinPlateSpline.o
ThinPlateSpline.cpp: In function 'SEXPREC* ThinPlateRegistration(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
ThinPlateSpline.cpp:168:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned i=0; i < srX.size(); i++) {
^
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c Widget.cpp -o Widget.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c affine.cpp -o affine.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c connectedcomponents3D.cpp -o connectedcomponents3D.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c display.cpp -o display.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c filter.cpp -o filter.o
filter.cpp: In function 'void FindBlobs(const cv::Mat&, std::vector<std::vector<cv::Point_ > >&, 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, bool, double, double, std::vector<std::vector<cv::Point_ > >&, 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(noFilter); //change to bool
^
filter.cpp:1003:7: warning: unused variable 'filterminArea' [-Wunused-variable]
int filterminArea = Rcpp::as(filter_minArea);
^
filter.cpp:1004:7: warning: unused variable 'filtermaxArea' [-Wunused-variable]
int filtermaxArea = Rcpp::as(filter_maxArea);
^
filter.cpp:1005:7: warning: unused variable 'filterminThresh' [-Wunused-variable]
int filterminThresh = Rcpp::as(filter_minThresh);
^
filter.cpp:1006:7: warning: unused variable 'filtermaxThresh' [-Wunused-variable]
int filtermaxThresh = Rcpp::as(filter_maxThresh);
^
filter.cpp:1007:7: warning: unused variable 'filtereccentricity' [-Wunused-variable]
int filtereccentricity = Rcpp::as(filter_eccentricity);
^
In file included from C:\R\R-3\library\opencv\include/opencv2/core.hpp:58:0,
from C:\R\R-3\library\opencv\include/opencv2/opencv.hpp:52,
from filter.cpp:2:
C:\R\R-3\library\opencv\include/opencv2/core/types.hpp: In function 'SEXPREC* createTiles(SEXP, SEXP, SEXP, SEXP, SEXP)':
C:\R\R-3\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:\R\R-3\library\opencv\include/opencv2/core.hpp:58:0,
from C:\R\R-3\library\opencv\include/opencv2/opencv.hpp:52,
from filter.cpp:2:
C:\R\R-3\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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c flatfieldcorrection.cpp -o flatfieldcorrection.o
flatfieldcorrection.cpp: In function 'void getGain(int, int, int, std::vectorcv::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(display);
^
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c gauss_transform.cpp -o gauss_transform.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c gauss_transform_make_default.cpp -o gauss_transform_make_default.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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:203:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0; i< contours.size(); i++ ){
^
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(getNested);
^
getContour.cpp:728:5: warning: unused variable 'numOfSegments2' [-Wunused-variable]
int numOfSegments2 = contoursDist.size();
^
getContour.cpp:528:51: warning: 'depth' may be used uninitialized in this function [-Wmaybe-uninitialized]
img.convertTo(dist_CV_8UC3,CV_8UC1,255.0/(depth)); //-255.0/Min
^
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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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(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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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::vectorcv::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::vectorcv::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::vectorcv::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::vectorcv::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(nrows);
^
laplacianpyramidblending.cpp:560:7: warning: unused variable 'horizontaltiles' [-Wunused-variable]
int horizontaltiles = Rcpp::as(ncols);
^
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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::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::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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c matrix.cpp -o matrix.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c nonrigid.cpp -o nonrigid.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c normalization.cpp -o normalization.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c rigid.cpp -o rigid.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c transform.cpp -o transform.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c utils.cpp -o utils.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -c wavelet2d.cpp -o wavelet2d.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/R/R-3/include" -DNDEBUG -I"C:\R\R-3\library\opencv\include\opencv2" -I"C:\R\R-3\library\opencv\include" -I"C:\R\R-3\library\opencv\x86\mingw\bin" -I"C:\fftw/" -I../inst/include -I"C:/R/R-3/library/Rcpp/include" -IC:/R/R-3/library/Rcpp/include -O2 -Wall -mtune=core2 -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:/Rtools/mingw_32/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:\R\R-3\library\opencv\x86\mingw\lib -lopencv_calib3d451 -lopencv_core451 -lopencv_features2d451 -lopencv_flann451 -lopencv_highgui451 -lopencv_imgcodecs451 -lopencv_imgproc451 -lopencv_ml451 -lopencv_objdetect451 -lopencv_photo451 -lopencv_stitching451 -lopencv_video451 -lopencv_videoio451 -LC:\fftw/ -lfftw3-3 -L..inst/include/x64 -LC:/R/R-3/bin/i386 -lR
C:\fftw//libfftw3-3.dll: file not recognized: File format not recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'wholebrain'

• removing 'C:/R/R-3/library/wholebrain'
  Warning messages:
  1: In i.p(...) :
  installation of package ‘C:/temp/RtmpaYD1DI/file3af86cb57f42/wholebrain_0.1.1.tar.gz’ had non-zero exit status
  2: 1 components of ... were not used.

We detected these problematic arguments:

• args

Did you misspecify an argument?

[tractatus]

@Biglazyant you can see the error at the very end.

We detected these problematic arguments:

args
Did you misspecify an argument?

Devtools now uses the following to make sure Windows compiles for only 64 bit and not 32 and 64 bit.

devtools::install_github("tractatus/wholebrain", INSTALL_opts=c("--no-multiarch"))

[tractatus]

Alternatively you can also do:

library(devtools)
options(devtools.install.args = "--no-multiarch")   
install_github("tractatus/wholebrain")

[Eason521]

Installation failed: Could not resolve host: raw.githubusercontent.com

Can you help me with this problem？
My network is OK

[Eason521]

I have a problem installing with a local package

Warning in untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers

• installing source package 'wholebrain' ...
  ** libs

*** arch - i386
Error in ROpenCVLite::opencvConfig("cflags", arch = Sys.getenv("R_ARCH")) :
OpenCV is not installed on this system. Please use installOpenCV() to install it.
停止执行
C:/Rtools/usr/mingw_32/bin/g++ -std=c++0x -I"D:/Dev/R/R-331.3/include" -DNDEBUG -I"D:\Dev\fftw/" -I../inst/include -I"D:/Dev/R/R-3.3.3/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -ID:/Dev/R/R-3.3.3/library/Rcpp/include -O2 -Wall -mtune=core2 -c CThinPlateSpline.cpp -o CThinPlateSpline.o
sh: C:/Rtools/usr/mingw_32/bin/g++: No such file or directory
make: *** [D:/Dev/R/R-331.3/etc/i386/Makeconf:188: CThinPlateSpline.o] Error 127
Warning: 运行命令'make -f "Makevars.win" -f "D:/Dev/R/R-331.3/etc/i386/Makeconf" -f "D:/Dev/R/R-331.3/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="wholebrain.dll" OBJECTS="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"'的状态是2
ERROR: compilation failed for package 'wholebrain'

• removing 'D:/Dev/R/R-3.3.3/library/wholebrain'
  Warning messages:
  1: 运行命令'"D:/Dev/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "D:\Dev\R\R-3.3.3\library" "E:/软件/R_software/R_package/tractatus-wholebrain.tar.gz"'的状态是1
  2: In install.packages(files[tarballs], .libPaths()[1L], repos = NULL,

But the environment variable is configured, so I don't know how to modify this path

[tractatus]

Hi @Eason521
that github is not resolved as host would indicate that you are behind some sort of proxy. If you are at a university or similar talk to you IT department.

Regarding the local installation error.
It looks like the option command to devtools didnt work since it tries to compile for 32-bit architecture.

try

devtools::install_github("tractatus/wholebrain", INSTALL_opts=c("--no-multiarch"))

When you see i386 it means 32-bit.
You want it to compile for 64-bit, x86.