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###
### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL methylKit
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'methylKit' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int, size_t&)':
methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized [-Wmaybe-uninitialized]
  687 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:24: note: 'CHGout' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
  686 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:15: note: 'CHHout' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:685:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
  685 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:547:9: note: 'out' was declared here
  547 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)':
methCall.cpp:1014:39: warning: 'CHGout' may be used uninitialized [-Wmaybe-uninitialized]
 1014 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:24: note: 'CHGout' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
 1013 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:15: note: 'CHHout' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:1012:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
 1012 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:827:9: note: 'out' was declared here
  827 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, size_t&)':
methCall.cpp:1244:39: warning: 'CHGout' may be used uninitialized [-Wmaybe-uninitialized]
 1244 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1142:24: note: 'CHGout' was declared here
 1142 |   FILE *out, *CHHout, *CHGout;
      |                        ^~~~~~
methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized [-Wmaybe-uninitialized]
 1243 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1142:15: note: 'CHHout' was declared here
 1142 |   FILE *out, *CHHout, *CHGout;
      |               ^~~~~~
methCall.cpp:1242:39: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized]
 1242 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1142:9: note: 'out' was declared here
 1142 |   FILE *out, *CHHout, *CHGout;
      |         ^~~
g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-methylKit/00new/methylKit/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylKit)