############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.20.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'methylKit' ... ** using staged installation ** libs "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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/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/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c methCall.cpp -o methCall.o methCall.cpp: In function 'int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int, size_t&)': methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); } ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:685:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp: In function 'int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, size_t&)': methCall.cpp:1014:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); } ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1042:76: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); } ~~~~~~~~~~~^~~~~ methCall.cpp: In function 'int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, size_t&)': methCall.cpp:1244:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); } ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1242:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.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/methylKit.buildbin-libdir/00LOCK-methylKit/00new/methylKit/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'methylKit' finding HTML links ... done PCASamples-methods html adjustMethylC html assocComp-methods html bedgraph-methods html calculateDiffMeth-methods html calculateDiffMethDSS-methods html clusterSamples-methods html dataSim-methods html diffMethPerChr-methods html extract-methods html filterByCoverage-methods html getAssembly-methods html getContext-methods html getCorrelation-methods html getCoverageStats-methods html getDBPath-methods html getData-methods html getMethylDiff-methods html getMethylationStats-methods html getSampleID-methods html getTreatment-methods html joinSegmentNeighbours html makeMethylDB-methods html methRead-methods html methSeg html finding level-2 HTML links ... done methSeg2bed html methylBase-class html methylBase.obj html methylBaseDB-class html methylDiff-class html methylDiff.obj html methylDiffDB-class html methylKit-defunct html methylRaw-class html methylRawDB-class html methylRawList-class html methylRawList.obj html methylRawListDB-class html normalizeCoverage-methods html percMethylation-methods html pool-methods html processBismarkAln-methods html readMethylDB-methods html reconstruct-methods html regionCounts html removeComp-methods html reorganize-methods html select-methods html selectByOverlap-methods html show-methods html tileMethylCounts-methods html unite-methods html updateMethObject 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 'methylKit' ... ** libs "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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/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/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c methCall.cpp -o methCall.o methCall.cpp: In function 'int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int, size_t&)': methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); } ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:685:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp: In function 'int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, size_t&)': methCall.cpp:1014:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); } ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1042:76: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); } ~~~~~~~~~~~^~~~~ methCall.cpp: In function 'int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, size_t&)': methCall.cpp:1244:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); } ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ methCall.cpp:1242:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized] if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);} ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.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/methylKit.buildbin-libdir/methylKit/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'methylKit' as methylKit_1.20.0.zip * DONE (methylKit)