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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:waddR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings waddR_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/waddR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'waddR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'waddR' version '1.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'waddR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/waddR/libs/x64/waddR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'waddR-Ex.R' failed
Warning in file(con, "r") :
  cannot open file 'waddR-Ex.Rout': Permission denied
Error in file(con, "r") : cannot open the connection
Execution halted

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL waddR
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'waddR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c wasserstein.cpp -o wasserstein.o
wasserstein.cpp: In function 'std::vector<double> rep_weighted(std::vector<double>, std::vector<int, std::allocator<int> >)':
wasserstein.cpp:348:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
      for(int i=0; i<x.size(); i++) {
                   ~^~~~~~~~~
wasserstein.cpp: In function 'std::vector<double> concat(std::vector<double>&, std::vector<double>&)':
wasserstein.cpp:386:27: warning: variable 'out_it_end' set but not used [-Wunused-but-set-variable]
  vector<double>::iterator out_it_end = out.end();
                           ^~~~~~~~~~
wasserstein.cpp: In function 'std::vector<int, std::allocator<int> > interval_table(const std::vector<double>&, const std::vector<double>&, int)':
wasserstein.cpp:584:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
    while (data_i < datavec.size()) {
           ~~~~~~~^~~~~~~~~~~~~~~~
wasserstein.cpp: In function 'double cor_test_export(Rcpp::NumericVector, Rcpp::NumericVector)':
wasserstein.cpp:1088:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for (int i=0; i<x.size(); i++) { x[i] = x_[i];}
                ~^~~~~~~~~
wasserstein.cpp:1089:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for (int j=0; j<y.size(); j++) { y[j] = y_[j];}
                ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'double cor(const std::vector<T>&, const std::vector<T>&, double, double) [with T = double]':
wasserstein.cpp:716:49:   required from here
wasserstein.cpp:439:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  for (int i=0; i<x.size(); i++){
wasserstein.cpp: In instantiation of 'std::vector<T> operator-(const std::vector<T>&, const std::vector<T>&) [with T = double]':
wasserstein.cpp:778:44:   required from here
wasserstein.cpp:121:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
wasserstein.cpp: In instantiation of 'std::vector<T> cumSum(const std::vector<T>&, int) [with T = double]':
wasserstein.cpp:884:17:   required from here
wasserstein.cpp:472:47: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  int upper = ((last_index > 0) && (last_index <= x.size())
                                   ~~~~~~~~~~~~^~~~~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> operator*(const std::vector<T>&, const std::vector<T>&) [with T = double]':
wasserstein.cpp:912:62:   required from here
wasserstein.cpp:101:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
wasserstein.cpp: In instantiation of 'std::vector<T> operator+(std::vector<T>, std::vector<T>) [with T = double]':
wasserstein.cpp:933:15:   required from here
wasserstein.cpp:53:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (int i=0; i<x.size(); i++) {
wasserstein.cpp: In instantiation of 'std::vector<T> operator/(const std::vector<T>&, const std::vector<T>&) [with T = double]':
wasserstein.cpp:1046:15:   required from here
wasserstein.cpp:169:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
wasserstein.cpp: In instantiation of 'std::vector<T> quantile(const std::vector<T>&, std::vector<double>, int) [with T = double]':
wasserstein.cpp:1162:27:   required from here
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
  T max_x = x_sorted[n-1];
    ^~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o waddR.dll tmp.def RcppExports.o wasserstein.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-waddR/00new/waddR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'waddR'
    finding HTML links ... done
    brownianBridgeEmpcdf.url                html  
    dot-brownianBridgeEmpcdf                html  
    dot-combinePVal                         html  
    dot-fishersCombinedPval                 html  
    dot-gpdFittedPValue                     html  
    dot-quantileCorrelation                 html  
    dot-relativeError                       html  
    dot-testWass                            html  
    dot-wassPermProcedure                   html  
    dot-wassersteinTestAsy                  html  
    dot-wassersteinTestSp                   html  
    permutations                            html  
    squared_wass_approx                     html  
    squared_wass_decomp                     html  
    testZeroes-method                       html  
    waddR-package                           html  
    wasserstein.sc-method                   html  
    wasserstein.test                        html  
    wasserstein_metric                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (waddR)
Making 'packages.html' ... done