Package: h5vc

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL h5vc

StartedAt: 2018-10-16 15:47:42 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 15:48:18 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 35.9 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL h5vc
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘h5vc’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
  int len = nttable->end - nttable->beg;
      ^
tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        }else if(p->indel > 0){
                 ^˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:64:16: note: uninitialized use occurs here
        str += c;
               ^
tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true
        }else if(p->indel > 0){
              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning
        char c;
              ^
               = '\0'
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
  int len = nttable->end - nttable->beg;
      ^
tallyBAM.cpp:141:6: warning: unused variable 'c' [-Wunused-variable]
        int c = 0;
            ^
tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function]
static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
           ^
5 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o h5vc.so tallyBAM.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/h5vc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘h5vc.simple.genome.browser.Rmd’ 
   ‘h5vc.tour.Rmd’ 
** testing if installed package can be loaded
* DONE (h5vc)