############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/qckitfastq_1.10.0.tar.gz && rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qckitfastq.buildbin-libdir qckitfastq_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL qckitfastq_1.10.0.zip && rm qckitfastq_1.10.0.tar.gz qckitfastq_1.10.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 747k 100 747k 0 0 1216k 0 --:--:-- --:--:-- --:--:-- 1219k install for i386 * installing *source* package 'qckitfastq' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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 >::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-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RSeqAn/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 >::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-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/qckitfastq.buildbin-libdir/qckitfastq/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'qckitfastq' as qckitfastq_1.10.0.zip * DONE (qckitfastq) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'qckitfastq' successfully unpacked and MD5 sums checked