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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:waddR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings waddR_1.12.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/waddR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'waddR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'waddR' version '1.12.0'
* 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 'F:/biocbuild/bbs-3.16-bioc/R/library/waddR/libs/x64/waddR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL waddR
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'waddR' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
  348 |      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]
  386 |  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]
  584 |    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]
 1088 |  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]
 1089 |  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]
  439 |  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]
  121 |     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]
  472 |  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]
  101 |     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]
   53 |   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]
  169 |     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]
  501 |  T max_x = x_sorted[n-1];
      |    ^~~~~
g++ -shared -s -static-libgcc -o waddR.dll tmp.def RcppExports.o wasserstein.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-waddR/00new/waddR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)