############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioQC_1.22.0.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioQC_1.22.0.zip && rm BioQC_1.22.0.tar.gz BioQC_1.22.0.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 3 4348k 3 165k 0 0 549k 0 0:00:07 --:--:-- 0:00:07 549k 34 4348k 34 1512k 0 0 1165k 0 0:00:03 0:00:01 0:00:02 1164k 86 4348k 86 3754k 0 0 1636k 0 0:00:02 0:00:02 --:--:-- 1636k 100 4348k 100 4348k 0 0 1749k 0 0:00:02 0:00:02 --:--:-- 1749k install for i386 * installing *source* package 'BioQC' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gini.c -o gini.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_gmt.cpp -o read_gmt.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stat_rank.c -o stat_rank.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c wmw_test.c -o wmw_test.o wmw_test.c: In function 'wmw_test_list': wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function 'wmw_test': wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function 'signed_wmw_test_list': wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function 'signed_wmw_test': wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -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/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BioQC' finding HTML links ... done BaseIndexList-class html GmtList-class html GmtList html IndexList-class html IndexList html SignedGenesets-class html SignedGenesets html SignedIndexList-class html SignedIndexList html absLog10p html appendGmtList html as.GmtList html entropy html entropyDiversity html entropySpecificity html filterBySize html filterPmat html getLeadingEdgeIndexFromVector html gini html gmtlist2signedGenesets html gsDesc html gsGeneCount html gsGenes html gsName html gsNamespace html hasNamespace html isValidBaseIndexList html isValidGmtList html isValidIndexList html isValidSignedGenesets html isValidSignedIndexList html matchGenes html offset-set html offset html prettySigNames html readCurrentSignatures html readGmt html readSignedGmt html sampleSpecialization html setDescAsNamespace html setGsNamespace html setNamespace html show-GmtList-method html show-IndexList-method html show-SignedGenesets-method html show-SignedIndexList-method html simplifyMatrix html sub-.GmtList html sub-sub-.GmtList html uniqGenesetsByNamespace html valTypes html wmwLeadingEdge html wmwTest html wmwTestInR html *** copying figures ** 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 'BioQC' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gini.c -o gini.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_gmt.cpp -o read_gmt.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stat_rank.c -o stat_rank.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c wmw_test.c -o wmw_test.o wmw_test.c: In function 'wmw_test_list': wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function 'wmw_test': wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function 'signed_wmw_test_list': wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function 'signed_wmw_test': wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -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/BioQC.buildbin-libdir/BioQC/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BioQC' as BioQC_1.22.0.zip * DONE (BioQC) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'BioQC' successfully unpacked and MD5 sums checked