* installing *source* package ‘qtl’ ...
** package ‘qtl’ successfully unpacked and MD5 sums checked
** libs
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c countXO.c -o countXO.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c discan.c -o discan.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c discan_covar.c -o discan_covar.o
discan_covar.c:119:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
discan_covar.c:123:9: note: uninitialized use occurs here
               Addcov, *n_addcov, Intcov, *n_intcov, pheno,
               ^~~~~~
discan_covar.c:119:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
discan_covar.c:116:31: note: initialize the variable 'Addcov' to silence this warning
  double ***Genoprob, **Addcov, **Intcov;
                              ^
                               = NULL
discan_covar.c:120:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
discan_covar.c:123:28: note: uninitialized use occurs here
               Addcov, *n_addcov, Intcov, *n_intcov, pheno,
                                  ^~~~~~
discan_covar.c:120:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
discan_covar.c:116:41: note: initialize the variable 'Intcov' to silence this warning
  double ***Genoprob, **Addcov, **Intcov;
                                        ^
                                         = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c effectscan.c -o effectscan.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c fill_geno_nodblXO.c -o fill_geno_nodblXO.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c findDupMarkers_notexact.c -o findDupMarkers_notexact.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c fitqtl_hk.c -o fitqtl_hk.o
fitqtl_hk.c:71:6: warning: variable 'Cov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
     ^~~~~~~~~~~
fitqtl_hk.c:74:7: note: uninitialized use occurs here
             Cov, *n_cov, model, *n_int, pheno, *get_ests, lod, df,
             ^~~
fitqtl_hk.c:71:3: note: remove the 'if' if its condition is always true
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
  ^~~~~~~~~~~~~~~~
fitqtl_hk.c:52:30: note: initialize the variable 'Cov' to silence this warning
  double ***Genoprob=0, **Cov;
                             ^
                              = NULL
fitqtl_hk.c:147:6: warning: variable 'Ests_covar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(get_ests) 
     ^~~~~~~~
fitqtl_hk.c:167:32: note: uninitialized use occurs here
                          sizefull, get_ests, ests, Ests_covar,
                                                    ^~~~~~~~~~
fitqtl_hk.c:147:3: note: remove the 'if' if its condition is always true
  if(get_ests) 
  ^~~~~~~~~~~~~
fitqtl_hk.c:125:30: note: initialize the variable 'Ests_covar' to silence this warning
  double *dwork, **Ests_covar;
                             ^
                              = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c fitqtl_hk_binary.c -o fitqtl_hk_binary.o
fitqtl_hk_binary.c:72:6: warning: variable 'Cov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
     ^~~~~~~~~~~
fitqtl_hk_binary.c:75:6: note: uninitialized use occurs here
                   Cov, *n_cov, model, *n_int, pheno, *get_ests, lod, df,
                   ^~~
fitqtl_hk_binary.c:72:3: note: remove the 'if' if its condition is always true
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
  ^~~~~~~~~~~~~~~~
fitqtl_hk_binary.c:53:30: note: initialize the variable 'Cov' to silence this warning
  double ***Genoprob=0, **Cov;
                             ^
                              = NULL
fitqtl_hk_binary.c:152:6: warning: variable 'Ests_covar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(get_ests) 
     ^~~~~~~~
fitqtl_hk_binary.c:172:35: note: uninitialized use occurs here
                      sizefull, get_ests, ests, Ests_covar,
                                                ^~~~~~~~~~
fitqtl_hk_binary.c:152:3: note: remove the 'if' if its condition is always true
  if(get_ests) 
  ^~~~~~~~~~~~~
fitqtl_hk_binary.c:130:30: note: initialize the variable 'Ests_covar' to silence this warning
  double *dwork, **Ests_covar;
                             ^
                              = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c fitqtl_imp.c -o fitqtl_imp.o
fitqtl_imp.c:62:6: warning: variable 'Cov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
     ^~~~~~~~~~~
fitqtl_imp.c:65:7: note: uninitialized use occurs here
             Cov, *n_cov, model, *n_int, pheno, *get_ests, lod, df,
             ^~~
fitqtl_imp.c:62:3: note: remove the 'if' if its condition is always true
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
  ^~~~~~~~~~~~~~~~
fitqtl_imp.c:55:15: note: initialize the variable 'Cov' to silence this warning
  double **Cov;
              ^
               = NULL
1 warning generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c fitqtl_imp_binary.c -o fitqtl_imp_binary.o
fitqtl_imp_binary.c:64:6: warning: variable 'Cov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
     ^~~~~~~~~~~
fitqtl_imp_binary.c:67:7: note: uninitialized use occurs here
                    Cov, *n_cov, model, *n_int, pheno, *get_ests, lod, df,
                    ^~~
fitqtl_imp_binary.c:64:3: note: remove the 'if' if its condition is always true
  if(*n_cov != 0) reorg_errlod(*n_ind, *n_cov, cov, &Cov);
  ^~~~~~~~~~~~~~~~
fitqtl_imp_binary.c:57:15: note: initialize the variable 'Cov' to silence this warning
  double **Cov;
              ^
               = NULL
1 warning generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c forwsel.c -o forwsel.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_4way.c -o hmm_4way.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_bc.c -o hmm_bc.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_bci.c -o hmm_bci.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_bgmagic16.c -o hmm_bgmagic16.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_f2.c -o hmm_f2.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_f2i.c -o hmm_f2i.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_main.c -o hmm_main.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_ri4self.c -o hmm_ri4self.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_ri4sib.c -o hmm_ri4sib.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_ri8self.c -o hmm_ri8self.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c hmm_ri8sib.c -o hmm_ri8sib.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c inferFounderHap.c -o inferFounderHap.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c info.c -o info.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c lapackutil.c -o lapackutil.o
lapackutil.c:57:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    if(abs(x0[*n_ind*i+i]) < TOL) {
       ~~~ ^~~~~~~~~~~~~~
1 warning generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c markerlrt.c -o markerlrt.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmaugment.cpp -o mqmaugment.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmdatatypes.cpp -o mqmdatatypes.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmeliminate.cpp -o mqmeliminate.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmmapqtl.cpp -o mqmmapqtl.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmmixture.cpp -o mqmmixture.o
mqmmixture.cpp:78:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
            else weight[i]*= 0.25;
            ^
1 warning generated.
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmprob.cpp -o mqmprob.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmregression.cpp -o mqmregression.o
clang++ -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c mqmscan.cpp -o mqmscan.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c pickMarkerSubset.c -o pickMarkerSubset.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c ril48_reorg.c -o ril48_reorg.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c ripple.c -o ripple.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_ehk.c -o scanone_ehk.o
scanone_ehk.c:65:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scanone_ehk.c:68:8: note: uninitialized use occurs here
              Intcov, *n_intcov, pheno, weights, result, *maxit, 
              ^~~~~~
scanone_ehk.c:65:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scanone_ehk.c:59:41: note: initialize the variable 'Intcov' to silence this warning
  double ***Genoprob, **Addcov, **Intcov;
                                        ^
                                         = NULL
scanone_ehk.c:64:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scanone_ehk.c:67:49: note: uninitialized use occurs here
  scanone_ehk(*n_ind, *n_pos, *n_gen, Genoprob, Addcov, *n_addcov,
                                                ^~~~~~
scanone_ehk.c:64:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scanone_ehk.c:59:31: note: initialize the variable 'Addcov' to silence this warning
  double ***Genoprob, **Addcov, **Intcov;
                              ^
                               = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_em.c -o scanone_em.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_em_covar.c -o scanone_em_covar.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_hk.c -o scanone_hk.o
scanone_hk.c:65:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scanone_hk.c:68:48: note: uninitialized use occurs here
  scanone_hk(*n_ind, *n_pos, *n_gen, Genoprob, Addcov, *n_addcov,
                                               ^~~~~~
scanone_hk.c:65:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scanone_hk.c:59:41: note: initialize the variable 'Addcov' to silence this warning
  double ***Genoprob, **Result, **Addcov, **Intcov;
                                        ^
                                         = NULL
scanone_hk.c:66:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scanone_hk.c:69:7: note: uninitialized use occurs here
             Intcov, *n_intcov, pheno, *nphe, weights, Result, 
             ^~~~~~
scanone_hk.c:66:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scanone_hk.c:59:51: note: initialize the variable 'Intcov' to silence this warning
  double ***Genoprob, **Result, **Addcov, **Intcov;
                                                  ^
                                                   = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_hk_binary.c -o scanone_hk_binary.o
scanone_hk_binary.c:63:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scanone_hk_binary.c:66:55: note: uninitialized use occurs here
  scanone_hk_binary(*n_ind, *n_pos, *n_gen, Genoprob, Addcov, *n_addcov,
                                                      ^~~~~~
scanone_hk_binary.c:63:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scanone_hk_binary.c:58:31: note: initialize the variable 'Addcov' to silence this warning
  double ***Genoprob, **Addcov, **Intcov;
                              ^
                               = NULL
scanone_hk_binary.c:64:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scanone_hk_binary.c:67:7: note: uninitialized use occurs here
                    Intcov, *n_intcov, pheno, result, *tol, *maxit, 
                    ^~~~~~
scanone_hk_binary.c:64:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scanone_hk_binary.c:58:41: note: initialize the variable 'Intcov' to silence this warning
  double ***Genoprob, **Addcov, **Intcov;
                                        ^
                                         = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_imp.c -o scanone_imp.o
scanone_imp.c:71:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov != 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~~
scanone_imp.c:75:8: note: uninitialized use occurs here
              Addcov, *n_addcov, Intcov, *n_intcov, pheno, *nphe, weights,
              ^~~~~~
scanone_imp.c:71:3: note: remove the 'if' if its condition is always true
  if(*n_addcov != 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~~
scanone_imp.c:64:18: note: initialize the variable 'Addcov' to silence this warning
  double **Addcov, **Intcov, **Result;
                 ^
                  = NULL
scanone_imp.c:72:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov != 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~~
scanone_imp.c:75:27: note: uninitialized use occurs here
              Addcov, *n_addcov, Intcov, *n_intcov, pheno, *nphe, weights,
                                 ^~~~~~
scanone_imp.c:72:3: note: remove the 'if' if its condition is always true
  if(*n_intcov != 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~~
scanone_imp.c:64:28: note: initialize the variable 'Intcov' to silence this warning
  double **Addcov, **Intcov, **Result;
                           ^
                            = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_mr.c -o scanone_mr.o
scanone_mr.c:65:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scanone_mr.c:68:7: note: uninitialized use occurs here
             Intcov, *n_intcov, pheno, weights, result);
             ^~~~~~
scanone_mr.c:65:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scanone_mr.c:59:28: note: initialize the variable 'Intcov' to silence this warning
  double **Addcov, **Intcov;
                           ^
                            = NULL
scanone_mr.c:64:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scanone_mr.c:67:44: note: uninitialized use occurs here
  scanone_mr(*n_ind, *n_pos, *n_gen, Geno, Addcov, *n_addcov,
                                           ^~~~~~
scanone_mr.c:64:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scanone_mr.c:59:18: note: initialize the variable 'Addcov' to silence this warning
  double **Addcov, **Intcov;
                 ^
                  = NULL
2 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scanone_np.c -o scanone_np.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scantwo_binary_em.c -o scantwo_binary_em.o
scantwo_binary_em.c:71:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_binary_em.c:74:24: note: uninitialized use occurs here
                         Addcov, *n_addcov, Intcov, *n_intcov, 
                                            ^~~~~~
scantwo_binary_em.c:71:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_em.c:64:38: note: initialize the variable 'Intcov' to silence this warning
  double **Result, **Addcov, **Intcov, *****Pairprob;
                                     ^
                                      = NULL
scantwo_binary_em.c:70:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_binary_em.c:74:5: note: uninitialized use occurs here
                         Addcov, *n_addcov, Intcov, *n_intcov, 
                         ^~~~~~
scantwo_binary_em.c:70:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_em.c:64:28: note: initialize the variable 'Addcov' to silence this warning
  double **Result, **Addcov, **Intcov, *****Pairprob;
                           ^
                            = NULL
scantwo_binary_em.c:311:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_binary_em.c:315:27: note: uninitialized use occurs here
                         Genoprob1, Genoprob2, Addcov, *n_addcov, 
                                               ^~~~~~
scantwo_binary_em.c:311:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_em.c:302:47: note: initialize the variable 'Addcov' to silence this warning
  double **Result_full, **Result_add, **Addcov, **Intcov;
                                              ^
                                               = NULL
scantwo_binary_em.c:312:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_binary_em.c:316:5: note: uninitialized use occurs here
                         Intcov, *n_intcov, pheno, start,
                         ^~~~~~
scantwo_binary_em.c:312:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_em.c:302:57: note: initialize the variable 'Intcov' to silence this warning
  double **Result_full, **Result_add, **Addcov, **Intcov;
                                                        ^
                                                         = NULL
4 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scantwo_binary_hk.c -o scantwo_binary_hk.o
scantwo_binary_hk.c:69:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_binary_hk.c:72:24: note: uninitialized use occurs here
                         Addcov, *n_addcov, Intcov, *n_intcov, 
                                            ^~~~~~
scantwo_binary_hk.c:69:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_hk.c:61:51: note: initialize the variable 'Intcov' to silence this warning
  double ***Genoprob, **Result, **Addcov, **Intcov, *****Pairprob;
                                                  ^
                                                   = NULL
scantwo_binary_hk.c:68:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_binary_hk.c:72:5: note: uninitialized use occurs here
                         Addcov, *n_addcov, Intcov, *n_intcov, 
                         ^~~~~~
scantwo_binary_hk.c:68:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_hk.c:61:41: note: initialize the variable 'Addcov' to silence this warning
  double ***Genoprob, **Result, **Addcov, **Intcov, *****Pairprob;
                                        ^
                                         = NULL
scantwo_binary_hk.c:420:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_binary_hk.c:423:46: note: uninitialized use occurs here
                         Genoprob1, Genoprob2, Addcov, *n_addcov, Intcov, 
                                                                  ^~~~~~
scantwo_binary_hk.c:420:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_hk.c:411:28: note: initialize the variable 'Intcov' to silence this warning
  double **Addcov, **Intcov;
                           ^
                            = NULL
scantwo_binary_hk.c:419:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_binary_hk.c:423:27: note: uninitialized use occurs here
                         Genoprob1, Genoprob2, Addcov, *n_addcov, Intcov, 
                                               ^~~~~~
scantwo_binary_hk.c:419:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_binary_hk.c:411:18: note: initialize the variable 'Addcov' to silence this warning
  double **Addcov, **Intcov;
                 ^
                  = NULL
4 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scantwo_em.c -o scantwo_em.o
scantwo_em.c:68:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_em.c:72:5: note: uninitialized use occurs here
                  Addcov, *n_addcov, Intcov, *n_intcov, 
                  ^~~~~~
scantwo_em.c:68:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_em.c:62:28: note: initialize the variable 'Addcov' to silence this warning
  double **Result, **Addcov, **Intcov, *****Pairprob;
                           ^
                            = NULL
scantwo_em.c:69:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_em.c:72:24: note: uninitialized use occurs here
                  Addcov, *n_addcov, Intcov, *n_intcov, 
                                     ^~~~~~
scantwo_em.c:69:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_em.c:62:38: note: initialize the variable 'Intcov' to silence this warning
  double **Result, **Addcov, **Intcov, *****Pairprob;
                                     ^
                                      = NULL
scantwo_em.c:340:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_em.c:344:5: note: uninitialized use occurs here
                  Intcov, *n_intcov, pheno, weights, 
                  ^~~~~~
scantwo_em.c:340:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_em.c:330:57: note: initialize the variable 'Intcov' to silence this warning
  double **Result_full, **Result_add, **Addcov, **Intcov;
                                                        ^
                                                         = NULL
scantwo_em.c:339:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_em.c:343:27: note: uninitialized use occurs here
                  Genoprob1, Genoprob2, Addcov, *n_addcov, 
                                        ^~~~~~
scantwo_em.c:339:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_em.c:330:47: note: initialize the variable 'Addcov' to silence this warning
  double **Result_full, **Result_add, **Addcov, **Intcov;
                                              ^
                                               = NULL
4 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scantwo_hk.c -o scantwo_hk.o
scantwo_hk.c:69:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_hk.c:72:24: note: uninitialized use occurs here
                  Addcov, *n_addcov, Intcov, *n_intcov, 
                                     ^~~~~~
scantwo_hk.c:69:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_hk.c:61:52: note: initialize the variable 'Intcov' to silence this warning
  double ***Genoprob, ***Result, **Addcov, **Intcov, *****Pairprob;
                                                   ^
                                                    = NULL
scantwo_hk.c:68:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_hk.c:72:5: note: uninitialized use occurs here
                  Addcov, *n_addcov, Intcov, *n_intcov, 
                  ^~~~~~
scantwo_hk.c:68:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_hk.c:61:42: note: initialize the variable 'Addcov' to silence this warning
  double ***Genoprob, ***Result, **Addcov, **Intcov, *****Pairprob;
                                         ^
                                          = NULL
scantwo_hk.c:431:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_hk.c:434:46: note: uninitialized use occurs here
                  Genoprob1, Genoprob2, Addcov, *n_addcov, Intcov, 
                                                           ^~~~~~
scantwo_hk.c:431:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_hk.c:422:28: note: initialize the variable 'Intcov' to silence this warning
  double **Addcov, **Intcov;
                           ^
                            = NULL
scantwo_hk.c:430:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_hk.c:434:27: note: uninitialized use occurs here
                  Genoprob1, Genoprob2, Addcov, *n_addcov, Intcov, 
                                        ^~~~~~
scantwo_hk.c:430:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_hk.c:422:18: note: initialize the variable 'Addcov' to silence this warning
  double **Addcov, **Intcov;
                 ^
                  = NULL
4 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scantwo_imp.c -o scantwo_imp.o
scantwo_imp.c:71:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov != 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~~
scantwo_imp.c:76:34: note: uninitialized use occurs here
              *n_draws, Draws1, Draws2, Addcov, *n_addcov, 
                                        ^~~~~~
scantwo_imp.c:71:3: note: remove the 'if' if its condition is always true
  if(*n_addcov != 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~~
scantwo_imp.c:63:18: note: initialize the variable 'Addcov' to silence this warning
  double **Addcov, **Intcov;
                 ^
                  = NULL
scantwo_imp.c:72:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov != 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~~
scantwo_imp.c:77:8: note: uninitialized use occurs here
              Intcov, *n_intcov, pheno, *nphe, weights, result,
              ^~~~~~
scantwo_imp.c:72:3: note: remove the 'if' if its condition is always true
  if(*n_intcov != 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~~
scantwo_imp.c:63:28: note: initialize the variable 'Intcov' to silence this warning
  double **Addcov, **Intcov;
                           ^
                            = NULL
scantwo_imp.c:67:6: warning: variable 'Draws2' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(!(*same_chr)) reorg_draws(*n_ind, *n_pos2, *n_draws, draws2, &Draws2);
     ^~~~~~~~~~~~
scantwo_imp.c:76:26: note: uninitialized use occurs here
              *n_draws, Draws1, Draws2, Addcov, *n_addcov, 
                                ^~~~~~
scantwo_imp.c:67:3: note: remove the 'if' if its condition is always true
  if(!(*same_chr)) reorg_draws(*n_ind, *n_pos2, *n_draws, draws2, &Draws2);
  ^~~~~~~~~~~~~~~~~
scantwo_imp.c:62:27: note: initialize the variable 'Draws2' to silence this warning
  int ***Draws1, ***Draws2;
                          ^
                           = NULL
3 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c scantwo_mr.c -o scantwo_mr.o
scantwo_mr.c:68:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_mr.c:71:5: note: uninitialized use occurs here
                  Intcov, *n_intcov, pheno, weights, Result,
                  ^~~~~~
scantwo_mr.c:68:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_mr.c:61:38: note: initialize the variable 'Intcov' to silence this warning
  double **Result, **Addcov, **Intcov;
                                     ^
                                      = NULL
scantwo_mr.c:67:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_mr.c:70:49: note: uninitialized use occurs here
  scantwo_1chr_mr(*n_ind, *n_pos, *n_gen, Geno, Addcov, *n_addcov, 
                                                ^~~~~~
scantwo_mr.c:67:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_mr.c:61:28: note: initialize the variable 'Addcov' to silence this warning
  double **Result, **Addcov, **Intcov;
                           ^
                            = NULL
scantwo_mr.c:347:6: warning: variable 'Addcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
     ^~~~~~~~~~~~~
scantwo_mr.c:351:19: note: uninitialized use occurs here
                  Geno1, Geno2, Addcov, *n_addcov, Intcov, 
                                ^~~~~~
scantwo_mr.c:347:3: note: remove the 'if' if its condition is always true
  if(*n_addcov > 0) reorg_errlod(*n_ind, *n_addcov, addcov, &Addcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_mr.c:339:47: note: initialize the variable 'Addcov' to silence this warning
  double **Result_full, **Result_add, **Addcov, **Intcov;
                                              ^
                                               = NULL
scantwo_mr.c:348:6: warning: variable 'Intcov' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
     ^~~~~~~~~~~~~
scantwo_mr.c:351:38: note: uninitialized use occurs here
                  Geno1, Geno2, Addcov, *n_addcov, Intcov, 
                                                   ^~~~~~
scantwo_mr.c:348:3: note: remove the 'if' if its condition is always true
  if(*n_intcov > 0) reorg_errlod(*n_ind, *n_intcov, intcov, &Intcov);
  ^~~~~~~~~~~~~~~~~~
scantwo_mr.c:339:57: note: initialize the variable 'Intcov' to silence this warning
  double **Result_full, **Result_add, **Addcov, **Intcov;
                                                        ^
                                                         = NULL
4 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c simulate.c -o simulate.o
simulate.c:133:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  max_chi = qpois(1e-10, L/50.0*(double)(m+2), 0, 0);
          ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/ripley/R/R-clang/include/Rmath.h:304:16: note: expanded from macro 'qpois'
#define qpois           Rf_qpois
                        ^
simulate.c:144:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    n_chi = rpois(L/50.0*(double)(m+1)*(1.0-p));
          ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/ripley/R/R-clang/include/Rmath.h:328:16: note: expanded from macro 'rpois'
#define rpois           Rf_rpois
                        ^
simulate.c:148:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
      n_ni_xo = rpois(L/100.0*p);
              ~ ^~~~~~~~~~~~~~~~
/Users/ripley/R/R-clang/include/Rmath.h:328:16: note: expanded from macro 'rpois'
#define rpois           Rf_rpois
                        ^
3 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c simulate_ril.c -o simulate_ril.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c stahl_mf.c -o stahl_mf.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c summary_scantwo.c -o summary_scantwo.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c util.c -o util.o
util.c:556:6: warning: variable 'Left' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:28: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                                  ^~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:552:28: note: initialize the variable 'Left' to silence this warning
  double **Location, **Left, **Right;
                           ^
                            = NULL
util.c:556:6: warning: variable 'gRight' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:48: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                                                      ^~~~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:551:61: note: initialize the variable 'gRight' to silence this warning
  int **Geno, **iLeft, **iRight, **nTyped, **gLeft, **gRight;
                                                            ^
                                                             = NULL
util.c:556:6: warning: variable 'gLeft' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:41: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                                               ^~~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:551:51: note: initialize the variable 'gLeft' to silence this warning
  int **Geno, **iLeft, **iRight, **nTyped, **gLeft, **gRight;
                                                  ^
                                                   = NULL
util.c:556:6: warning: variable 'nTyped' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:56: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                                                              ^~~~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:551:42: note: initialize the variable 'nTyped' to silence this warning
  int **Geno, **iLeft, **iRight, **nTyped, **gLeft, **gRight;
                                         ^
                                          = NULL
util.c:556:6: warning: variable 'Right' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:34: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                                        ^~~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:552:37: note: initialize the variable 'Right' to silence this warning
  double **Location, **Left, **Right;
                                    ^
                                     = NULL
util.c:556:6: warning: variable 'iRight' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:20: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                          ^~~~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:551:32: note: initialize the variable 'iRight' to silence this warning
  int **Geno, **iLeft, **iRight, **nTyped, **gLeft, **gRight;
                               ^
                                = NULL
util.c:556:6: warning: variable 'iLeft' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(*full_info) {
     ^~~~~~~~~~
util.c:567:13: note: uninitialized use occurs here
            nseen, iLeft, iRight, Left, Right, gLeft, gRight, nTyped, *full_info);
                   ^~~~~
util.c:556:3: note: remove the 'if' if its condition is always true
  if(*full_info) {
  ^~~~~~~~~~~~~~~
util.c:551:22: note: initialize the variable 'iLeft' to silence this warning
  int **Geno, **iLeft, **iRight, **nTyped, **gLeft, **gRight;
                     ^
                      = NULL
7 warnings generated.
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c vbscan.c -o vbscan.o
clang -mtune=native -I/Users/ripley/R/R-clang/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c zeroin.c -o zeroin.o
clang++ -mtune=native -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qtl.so countXO.o discan.o discan_covar.o effectscan.o fill_geno_nodblXO.o findDupMarkers_notexact.o fitqtl_hk.o fitqtl_hk_binary.o fitqtl_imp.o fitqtl_imp_binary.o forwsel.o hmm_4way.o hmm_bc.o hmm_bci.o hmm_bgmagic16.o hmm_f2.o hmm_f2i.o hmm_main.o hmm_ri4self.o hmm_ri4sib.o hmm_ri8self.o hmm_ri8sib.o inferFounderHap.o info.o lapackutil.o markerlrt.o mqmaugment.o mqmdatatypes.o mqmeliminate.o mqmmapqtl.o mqmmixture.o mqmprob.o mqmregression.o mqmscan.o pickMarkerSubset.o ril48_reorg.o ripple.o scanone_ehk.o scanone_em.o scanone_em_covar.o scanone_hk.o scanone_hk_binary.o scanone_imp.o scanone_mr.o scanone_np.o scantwo_binary_em.o scantwo_binary_hk.o scantwo_em.o scantwo_hk.o scantwo_imp.o scantwo_mr.o simulate.o simulate_ril.o stahl_mf.o summary_scantwo.o util.o vbscan.o zeroin.o -L/Users/ripley/R/R-clang/lib -lRlapack -L/Users/ripley/R/R-clang/lib -lRblas -L/usr/lib/gcc/i686-apple-darwin11/4.2.1/x86_64 -L/usr/lib/gcc/i686-apple-darwin11/4.2.1 -L/usr/lib -lgfortran -L/Users/ripley/R/R-clang/lib -lR -dylib_file libRblas.dylib:/Users/ripley/R/R-clang/lib/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
installing to /Users/ripley/R/packages/tests-clang/qtl.Rcheck/qtl/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (qtl)