############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/mitoClone2_1.0.0.tar.gz && rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mitoClone2.buildbin-libdir mitoClone2_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL mitoClone2_1.0.0.zip && rm mitoClone2_1.0.0.tar.gz mitoClone2_1.0.0.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 930k 100 930k 0 0 1185k 0 --:--:-- --:--:-- --:--:-- 1187k install for i386 * installing *source* package 'mitoClone2' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite ../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch] double gamma = 1; ^~~~~ ../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)': ../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" cp scite "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" rm scite "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R_10x.cpp -o bam2R_10x.o bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment] /************************************************************************************** bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment] /********************************************************************** bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map, std::vector >&)': bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable] int bc_absent; ^~~~~~~~~ bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable] hts_itr_t *iter = NULL; ^~~~ bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -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/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'mitoClone2' finding HTML links ... done bam2R_10x html baseCountsFromBamList html clusterMetaclones html data html getAlleleCount html getCloneLikelihood html getVarsCandidate html mitoPlot html mut2GR html mutationCalls-class html mutationCallsFromCohort html mutationCallsFromExclusionlist html mutationCallsFromMatrix html overwriteMetaclones html plotClones html pullcountsVars html quick_cluster html removeWindow html setVarsCandidate html varCluster 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 'mitoClone2' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite ../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch] double gamma = 1; ^~~~~ ../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)': ../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/SCITE/" cp scite "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/SCITE/" rm scite "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R_10x.cpp -o bam2R_10x.o bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment] /************************************************************************************** bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment] /********************************************************************** bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map, std::vector >&)': bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable] int bc_absent; ^~~~~~~~~ bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable] hts_itr_t *iter = NULL; ^~~~ bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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/mitoClone2.buildbin-libdir/mitoClone2/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'mitoClone2' as mitoClone2_1.0.0.zip * DONE (mitoClone2) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'mitoClone2' successfully unpacked and MD5 sums checked