############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch esATAC ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' * installing *source* package 'esATAC' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BedLine.cpp -o BedLine.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BedUtils.cpp -o BedUtils.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChrDivi.cpp -o ChrDivi.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CutCountPre.cpp -o CutCountPre.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CutSiteCount.cpp -o CutSiteCount.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibComplexQC.cpp -o LibComplexQC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -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/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SortBed.cpp -o SortBed.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_wrapper.cpp -o rcpp_wrapper.o rcpp_wrapper.cpp: In function 'int CutSiteCount_wrapper(Rcpp::List)': rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable] int tmp_k; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c renamer.cpp -o renamer.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sam2bed.cc -o sam2bed.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o esATAC.dll tmp.def BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.13-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'esATAC' finding HTML links ... done ATACProc-class html BamToBed html BedToBigWig html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedToBigWig.html BedUtils html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedUtils.html Bowtie2Mapping html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bowtie2Mapping.html finding level-2 HTML links ... done CutSiteCountR html CutSitePre html FRiPQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fripQC.html FastQC html FindAdapter html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/findAdapter.html FragLenDistr html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fragLenDistr.html LibComplexQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/libComplexQC.html PeakCallingFseq html PeakQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/peakQC.html RGo html RMotifScan html RMotifScanPair html RPeakAnno html RPeakComp html RSNPs html RemoveAdapter html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/removeAdapter.html Renamer html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/renamer.html Rsortbam html SamToBam html SamToBed html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/samToBed.html SingleRepReport html TSSQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/tssQC.html UnzipAndMerge html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/unzipAndMerge.html atacPipe2 html atacRepsPipe html atacRepsPipe2 html esATAC-package html getMotifInfo html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled ** testing if installed package can be loaded from final location Warning in options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled ** testing if installed package keeps a record of temporary installation path * DONE (esATAC) Making 'packages.html' ... done