* using log directory 'd:/Rcompile/CRANpkg/local/3.6/rliger.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'rliger/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rliger' version '1.0.0'
* 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 'rliger' can be installed ... ERROR
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/rliger.Rcheck/00install.out' for details.
* DONE
The installation logfile:
* installing *source* package 'rliger' ...
** package 'rliger' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
make[1]: Entering directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-i386'
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c data_processing.cpp -o data_processing.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c fast_wilcox.cpp -o fast_wilcox.o
fast_wilcox.cpp: In function 'std::list<float> cpp_in_place_rank_mean(arma::vec&, int, int)':
fast_wilcox.cpp:118:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = idx_begin; i <= idx_end; i++) {
                                  ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c feature_mat.cpp -o feature_mat.o
feature_mat.cpp: In function 'Rcpp::NumericMatrix makeFeatureMatrix(Rcpp::DataFrame&, Rcpp::StringVector&)':
feature_mat.cpp:32:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0; i < barcodes_v.size(); ++i){
                    ^
feature_mat.cpp:44:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0; j < associated_barcodes.size(); ++j){
                    ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c quantile_norm.cpp -o quantile_norm.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c run_nmf.cpp -o run_nmf.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c snn.cpp -o snn.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -shared -s -static-libgcc -o rliger.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_processing.o fast_wilcox.o feature_mat.o quantile_norm.o run_nmf.o snn.o -LD:/RCompile/recent/R-3.6.3/bin/i386 -lRlapack -LD:/RCompile/recent/R-3.6.3/bin/i386 -lRblas -lgfortran -lm -lquadmath -Ld:/Compiler/gcc-4.9.3/local330/lib/i386 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R-3.6.3/bin/i386 -lR
make[1]: Leaving directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-i386'
make[1]: Entering directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-i386'
make[1]: Leaving directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-i386'
installing to d:/Rcompile/CRANpkg/lib/3.6/00LOCK-rliger/00new/rliger/libs/i386

*** arch - x64
make[1]: Entering directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-x64'
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c data_processing.cpp -o data_processing.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c fast_wilcox.cpp -o fast_wilcox.o
fast_wilcox.cpp: In function 'std::list<float> cpp_in_place_rank_mean(arma::vec&, int, int)':
fast_wilcox.cpp:118:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = idx_begin; i <= idx_end; i++) {
                                  ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c feature_mat.cpp -o feature_mat.o
feature_mat.cpp: In function 'Rcpp::NumericMatrix makeFeatureMatrix(Rcpp::DataFrame&, Rcpp::StringVector&)':
feature_mat.cpp:32:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0; i < barcodes_v.size(); ++i){
                    ^
feature_mat.cpp:44:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0; j < associated_barcodes.size(); ++j){
                    ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c quantile_norm.cpp -o quantile_norm.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c run_nmf.cpp -o run_nmf.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11 -I"D:/RCompile/recent/R-3.6.3/include" -DNDEBUG -DARMA_64BIT_WORD=1  -I"d:/RCompile/CRANpkg/lib/3.6/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppEigen/include" -I"d:/RCompile/CRANpkg/lib/3.6/RcppProgress/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -DARMA_DONT_USE_OPENMP    -O2 -Wall  -mtune=core2 -c snn.cpp -o snn.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -shared -s -static-libgcc -o rliger.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_processing.o fast_wilcox.o feature_mat.o quantile_norm.o run_nmf.o snn.o -LD:/RCompile/recent/R-3.6.3/bin/x64 -lRlapack -LD:/RCompile/recent/R-3.6.3/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R-3.6.3/bin/x64 -lR
make[1]: Leaving directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-x64'
make[1]: Entering directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-x64'
make[1]: Leaving directory `/cygdrive/d/temp/Rtmp8gIdMC/R.INSTALL19b0046d6529f/rliger/src-x64'
installing to d:/Rcompile/CRANpkg/lib/3.6/00LOCK-rliger/00new/rliger/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading

runtime error R6031
- Attempt to initialize the CRT more than once.
This indicates a bug in your application.
ERROR: lazy loading failed for package 'rliger'
* removing 'd:/Rcompile/CRANpkg/lib/3.6/rliger'
* restoring previous 'd:/Rcompile/CRANpkg/lib/3.6/rliger'