This page was generated on 2022-04-13 12:05:35 -0400 (Wed, 13 Apr 2022).
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL methylKit
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-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_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:1014:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1014 | if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1013 | if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1012:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1012 | if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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 in this function [-Wmaybe-uninitialized]
1244 | if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1243 | if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1242 | if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)