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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Rqc_1.22.0.tar.gz && rm -rf Rqc.buildbin-libdir && mkdir Rqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rqc.buildbin-libdir Rqc_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Rqc_1.22.0.zip && rm Rqc_1.22.0.tar.gz Rqc_1.22.0.zip
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install for i386

* installing *source* package 'Rqc' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function 'Rcpp::StringVector toRRDNA(Rcpp::StringVector)':
RRDNA.cpp:51:27: warning: comparison of integer expressions of different signedness: 'R_len_t' {aka 'int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
             for (j = 0; j < dna.size(); j+=3)
                         ~~^~~~~~~~~~~~
RRDNA.cpp: In function 'Rcpp::StringVector fromRRDNA(Rcpp::StringVector)':
RRDNA.cpp:102:22: warning: comparison of integer expressions of different signedness: 'R_len_t' {aka 'int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(j = 1; j < rrdna.size(); ++j) {
                    ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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 -shared -s -static-libgcc -o Rqc.dll tmp.def RRDNA.o RcppExports.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Rqc.buildbin-libdir/00LOCK-Rqc/00new/Rqc/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rqc'
    finding HTML links ... done
    Rqc-package                             html  
    RqcResultSet-class                      html  
    checkpoint                              html  
    detectFileFormat                        html  
    fromRRDNA                               html  
    matdist                                 html  
    rqc                                     html  
    finding level-2 HTML links ... done

    rqcCycleAverageQualityPcaPlot           html  
    rqcCycleAverageQualityPlot              html  
    rqcCycleBaseCallsPlot                   html  
    rqcCycleGCPlot                          html  
    rqcCycleQualityBoxPlot                  html  
    rqcCycleQualityPlot                     html  
    rqcFileHeatmap                          html  
    rqcGroupCycleAverageQualityPlot         html  
    rqcQA                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpc3yW8L/R.INSTALLb5451755711/Rqc/man/rqcQA.Rd:65: file link 'FastqFile' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpc3yW8L/R.INSTALLb5451755711/Rqc/man/rqcQA.Rd:66: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    rqcReadFrequencyPlot                    html  
    rqcReadQualityBoxPlot                   html  
    rqcReadQualityPlot                      html  
    rqcReadWidthPlot                        html  
    rqcReport                               html  
    rqcShinyReport                          html  
    stats4trim                              html  
    subsetByGroup                           html  
    subsetByPair                            html  
    toRRDNA                                 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 'Rqc' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function 'Rcpp::StringVector toRRDNA(Rcpp::StringVector)':
RRDNA.cpp:51:27: warning: comparison of integer expressions of different signedness: 'R_len_t' {aka 'int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
             for (j = 0; j < dna.size(); j+=3)
                         ~~^~~~~~~~~~~~
RRDNA.cpp: In function 'Rcpp::StringVector fromRRDNA(Rcpp::StringVector)':
RRDNA.cpp:102:22: warning: comparison of integer expressions of different signedness: 'R_len_t' {aka 'int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(j = 1; j < rrdna.size(); ++j) {
                    ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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 -shared -s -static-libgcc -o Rqc.dll tmp.def RRDNA.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Rqc.buildbin-libdir/Rqc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rqc' as Rqc_1.22.0.zip
* DONE (Rqc)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Rqc' successfully unpacked and MD5 sums checked