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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL methylKit
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)’:
methCall.cpp:1220:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1219:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1218:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int)’:
methCall.cpp:678:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:677:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:676:39: 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)’:
methCall.cpp:997:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:996:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:995:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-methylKit/00new/methylKit/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylKit)