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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL methylKit
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)’:
methCall.cpp:908:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
  908 |   for (i = 0; i < len_cigar; i++)
      |               ~~^~~~~~~~~~~
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 in this function [-Wmaybe-uninitialized]
  687 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  686 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  685 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)’:
methCall.cpp:1038:76: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1038 |   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
      |                                                                 ~~~~~~~~~~~^~~~~~~~
methCall.cpp:1037:76: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1037 |   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
      |                                                                 ~~~~~~~~~~~^~~~~~~~
methCall.cpp:1036:76: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1036 |   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
      |                                                                 ~~~~~~~~~~~^~~~~
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, size_t&)’:
methCall.cpp:1238:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1238 |       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1237:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1237 |       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1236:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1236 |       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)