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###
### Running command:
###
###   rm -rf bridge.buildbin-libdir && mkdir bridge.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bridge_1.58.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R bridge.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bridge.buildbin-libdir bridge_1.58.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bridge’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c:36:7: warning: unused variable 'old_model' [-Wunused-variable]
  int old_model;
      ^
bridge2.affy.c:37:7: warning: unused variable 'count_model' [-Wunused-variable]
  int count_model=0;
      ^
bridge2.affy.c:302:3: warning: implicit declaration of function 'dirichlet' is invalid in C99 [-Wimplicit-function-declaration]
  dirichlet(gamma, 2, w);
  ^
bridge2.affy.c:282:10: warning: unused variable 'w_new' [-Wunused-variable]
  double w_new[2];
         ^
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bridge2.c -o bridge2.o
bridge2.c:198:10: warning: unused variable 'old_b' [-Wunused-variable]
  double old_b=0,width_b=5;
         ^
bridge2.c:165:17: warning: unused variable 'l_ab_new' [-Wunused-variable]
  double l_ab=0,l_ab_new=0;
                ^
bridge2.c:165:10: warning: unused variable 'l_ab' [-Wunused-variable]
  double l_ab=0,l_ab_new=0;
         ^
bridge2.c:198:18: warning: unused variable 'width_b' [-Wunused-variable]
  double old_b=0,width_b=5;
                 ^
bridge2.c:199:18: warning: unused variable 'width_a' [-Wunused-variable]
  double old_a=0,width_a=5;
                 ^
bridge2.c:163:26: warning: unused variable 'post_prec_eta' [-Wunused-variable]
  double post_mean_eta=0,post_prec_eta=0;
                         ^
bridge2.c:199:10: warning: unused variable 'old_a' [-Wunused-variable]
  double old_a=0,width_a=5;
         ^
bridge2.c:154:10: warning: unused variable 'dens_t' [-Wunused-variable]
  double dens_t=0,dens_t_new=0;
         ^
bridge2.c:154:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
  double dens_t=0,dens_t_new=0;
                  ^
bridge2.c:171:7: warning: unused variable 'countrho' [-Wunused-variable]
  int countrho=0;
      ^
bridge2.c:166:22: warning: unused variable 'b_eps_new' [-Wunused-variable]
  double a_eps_new=0,b_eps_new=0;
                     ^
bridge2.c:166:10: warning: unused variable 'a_eps_new' [-Wunused-variable]
  double a_eps_new=0,b_eps_new=0;
         ^
bridge2.c:160:27: warning: unused variable 'post_prec_beta' [-Wunused-variable]
  double post_mean_beta=0,post_prec_beta=0;
                          ^
bridge2.c:159:25: warning: unused variable 'post_prec_mu' [-Wunused-variable]
  double post_mean_mu=0,post_prec_mu=0;
                        ^
bridge2.c:177:7: warning: unused variable 'countp' [-Wunused-variable]
  int countp=0;
      ^
bridge2.c:160:10: warning: unused variable 'post_mean_beta' [-Wunused-variable]
  double post_mean_beta=0,post_prec_beta=0;
         ^
bridge2.c:142:10: warning: unused variable 'sum_rho' [-Wunused-variable]
  double sum_rho=0,sum_rho_new=0;
         ^
bridge2.c:159:10: warning: unused variable 'post_mean_mu' [-Wunused-variable]
  double post_mean_mu=0,post_prec_mu=0;
         ^
bridge2.c:142:20: warning: unused variable 'sum_rho_new' [-Wunused-variable]
  double sum_rho=0,sum_rho_new=0;
                   ^
bridge2.c:175:7: warning: unused variable 'countb_eps' [-Wunused-variable]
  int countb_eps=0;
      ^
bridge2.c:138:10: warning: unused variable 'rho_new' [-Wunused-variable]
  double rho_new;
         ^
bridge2.c:174:7: warning: unused variable 'counta_eps' [-Wunused-variable]
  int counta_eps=0;
      ^
bridge2.c:143:10: warning: unused variable 'dens_rho' [-Wunused-variable]
  double dens_rho,dens_rho_new;
         ^
bridge2.c:143:19: warning: unused variable 'dens_rho_new' [-Wunused-variable]
  double dens_rho,dens_rho_new;
                  ^
bridge2.c:173:7: warning: unused variable 'counta' [-Wunused-variable]
  int counta=0;
      ^
bridge2.c:192:10: warning: unused variable 'sum_res2' [-Wunused-variable]
  double sum_res2;
         ^
bridge2.c:163:10: warning: unused variable 'post_mean_eta' [-Wunused-variable]
  double post_mean_eta=0,post_prec_eta=0;
         ^
bridge2.c:191:10: warning: unused variable 'sum_res1' [-Wunused-variable]
  double sum_res1;
         ^
bridge2.c:162:10: warning: unused variable 'post_mean_delta' [-Wunused-variable]
  double post_mean_delta=0,post_prec_delta=0;
         ^
bridge2.c:162:28: warning: unused variable 'post_prec_delta' [-Wunused-variable]
  double post_mean_delta=0,post_prec_delta=0;
                           ^
bridge2.c:161:28: warning: unused variable 'post_prec_alpha' [-Wunused-variable]
  double post_mean_alpha=0,post_prec_alpha=0;
                           ^
bridge2.c:145:10: warning: unused variable 'pi' [-Wunused-variable]
  double pi=3.14;
         ^
bridge2.c:161:10: warning: unused variable 'post_mean_alpha' [-Wunused-variable]
  double post_mean_alpha=0,post_prec_alpha=0;
         ^
33 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bridge2_util.c -o bridge2_util.o
bridge2_util.c:570:5: warning: implicit declaration of function 'dqrdc2_' is invalid in C99 [-Wimplicit-function-declaration]
    F77_CALL(dqrdc2)(xt, &n, &n, &p, &tol, &rank,qraux, pivot, work);
    ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x)    x ## _
                        ^
<scratch space>:77:1: note: expanded from here
dqrdc2_
^
bridge2_util.c:585:5: warning: implicit declaration of function 'dqrcf_' is invalid in C99 [-Wimplicit-function-declaration]
    F77_CALL(dqrcf)(xt, &n, &rank, qraux,yt, &n, coeft, &info);
    ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x)    x ## _
                        ^
<scratch space>:78:1: note: expanded from here
dqrcf_
^
bridge2_util.c:549:11: warning: unused variable 'vmax' [-Wunused-variable]
    char *vmax;
          ^
bridge2_util.c:608:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
bridge2_util.c:655:11: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k;
          ^
bridge2_util.c:693:5: warning: implicit declaration of function 'dqrdc2_' is invalid in C99 [-Wimplicit-function-declaration]
    F77_CALL(dqrdc2)(xtmp, &n, &n, &p, &tol, &rank,qraux, pivot, work);
    ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x)    x ## _
                        ^
<scratch space>:79:1: note: expanded from here
dqrdc2_
^
6 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bridge3.c -o bridge3.o
bridge3.c:38:7: warning: unused variable 'count_model' [-Wunused-variable]
  int count_model=0;
      ^
bridge3.c:37:7: warning: unused variable 'old_model' [-Wunused-variable]
  int old_model;
      ^
bridge3.c:332:25: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
  else if((w_star[3]<u) & u<w_star[4])
                        ^~~~~~~~~~~~~
bridge3.c:332:25: note: place parentheses around the '<' expression to silence this warning
  else if((w_star[3]<u) & u<w_star[4])
                        ^
                          (          )
bridge3.c:332:25: note: place parentheses around the & expression to evaluate it first
  else if((w_star[3]<u) & u<w_star[4])
                        ^
          (                )
bridge3.c:362:10: warning: unused variable 'w_new' [-Wunused-variable]
  double w_new[5];
         ^
4 warnings generated.
clang -mmacosx-version-min=10.13 -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 bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/bridge.buildbin-libdir/00LOCK-bridge/00new/bridge/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 (bridge)


>>>>>>> 
>>>>>>> FIXING LINKS FOR bridge.buildbin-libdir/bridge/libs/bridge.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "bridge.buildbin-libdir/bridge/libs/bridge.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "bridge.buildbin-libdir/bridge/libs/bridge.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "bridge.buildbin-libdir/bridge/libs/bridge.so"