##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qckitfastq.buildbin-libdir qckitfastq_1.8.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'qckitfastq' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c calc_adapter_content.cpp -o calc_adapter_content.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gzstream.cpp -o gzstream.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::__cxx11::string)':
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<int, std::vector<unsigned char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
                 if (pos_counter <= qual_score_matrix.size()) {
                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o qckitfastq.dll tmp.def RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/qckitfastq.buildbin-libdir/00LOCK-qckitfastq/00new/qckitfastq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qckitfastq'
    finding HTML links ... done
    GC_content                              html  
    adapter_content                         html  
    calc_adapter_content                    html  
    calc_format_score                       html  
    calc_over_rep_seq                       html  
    dimensions                              html  
    find_format                             html  
    gc_per_read                             html  
    kmer_count                              html  
    overrep_kmer                            html  
    overrep_reads                           html  
    per_base_quality                        html  
    per_read_quality                        html  
    plot_GC_content                         html  
    plot_adapter_content                    html  
    plot_outliers                           html  
    plot_overrep_kmer                       html  
    plot_overrep_reads                      html  
    plot_per_base_quality                   html  
    plot_per_read_quality                   html  
    plot_read_content                       html  
    plot_read_length                        html  
    qual_score_per_read                     html  
    read_base_content                       html  
    read_content                            html  
    read_length                             html  
    run_all                                 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

install for x64

* installing *source* package 'qckitfastq' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c calc_adapter_content.cpp -o calc_adapter_content.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gzstream.cpp -o gzstream.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::__cxx11::string)':
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<int, std::vector<unsigned char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                 if (pos_counter <= qual_score_matrix.size()) {
                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o qckitfastq.dll tmp.def RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/qckitfastq.buildbin-libdir/qckitfastq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qckitfastq' as qckitfastq_1.8.0.zip
* DONE (qckitfastq)