############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL bridge ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘bridge’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bridge2.affy.c -o bridge2.affy.o bridge2.affy.c: In function ‘gene_express_2s’: bridge2.affy.c:37:7: warning: unused variable ‘count_model’ [-Wunused-variable] 37 | int count_model=0; | ^~~~~~~~~~~ bridge2.affy.c:36:7: warning: unused variable ‘old_model’ [-Wunused-variable] 36 | int old_model; | ^~~~~~~~~ bridge2.affy.c: In function ‘up_date_w2’: bridge2.affy.c:302:3: warning: implicit declaration of function ‘dirichlet’; did you mean ‘dirichlet2’? [-Wimplicit-function-declaration] 302 | dirichlet(gamma, 2, w); | ^~~~~~~~~ | dirichlet2 bridge2.affy.c:282:10: warning: unused variable ‘w_new’ [-Wunused-variable] 282 | double w_new[2]; | ^~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bridge2.c -o bridge2.o bridge2.c: In function ‘mcmc’: bridge2.c:199:18: warning: unused variable ‘width_a’ [-Wunused-variable] 199 | double old_a=0,width_a=5; | ^~~~~~~ bridge2.c:199:10: warning: unused variable ‘old_a’ [-Wunused-variable] 199 | double old_a=0,width_a=5; | ^~~~~ bridge2.c:198:18: warning: unused variable ‘width_b’ [-Wunused-variable] 198 | double old_b=0,width_b=5; | ^~~~~~~ bridge2.c:198:10: warning: unused variable ‘old_b’ [-Wunused-variable] 198 | double old_b=0,width_b=5; | ^~~~~ bridge2.c:192:10: warning: unused variable ‘sum_res2’ [-Wunused-variable] 192 | double sum_res2; | ^~~~~~~~ bridge2.c:191:10: warning: unused variable ‘sum_res1’ [-Wunused-variable] 191 | double sum_res1; | ^~~~~~~~ bridge2.c:177:7: warning: unused variable ‘countp’ [-Wunused-variable] 177 | int countp=0; | ^~~~~~ bridge2.c:175:7: warning: unused variable ‘countb_eps’ [-Wunused-variable] 175 | int countb_eps=0; | ^~~~~~~~~~ bridge2.c:174:7: warning: unused variable ‘counta_eps’ [-Wunused-variable] 174 | int counta_eps=0; | ^~~~~~~~~~ bridge2.c:173:7: warning: unused variable ‘counta’ [-Wunused-variable] 173 | int counta=0; | ^~~~~~ bridge2.c:171:7: warning: unused variable ‘countrho’ [-Wunused-variable] 171 | int countrho=0; | ^~~~~~~~ bridge2.c:166:22: warning: unused variable ‘b_eps_new’ [-Wunused-variable] 166 | double a_eps_new=0,b_eps_new=0; | ^~~~~~~~~ bridge2.c:166:10: warning: unused variable ‘a_eps_new’ [-Wunused-variable] 166 | double a_eps_new=0,b_eps_new=0; | ^~~~~~~~~ bridge2.c:165:17: warning: unused variable ‘l_ab_new’ [-Wunused-variable] 165 | double l_ab=0,l_ab_new=0; | ^~~~~~~~ bridge2.c:165:10: warning: unused variable ‘l_ab’ [-Wunused-variable] 165 | double l_ab=0,l_ab_new=0; | ^~~~ bridge2.c:164:24: warning: variable ‘mean_gamma2’ set but not used [-Wunused-but-set-variable] 164 | double mean_gamma1=0,mean_gamma2=0; | ^~~~~~~~~~~ bridge2.c:164:10: warning: variable ‘mean_gamma1’ set but not used [-Wunused-but-set-variable] 164 | double mean_gamma1=0,mean_gamma2=0; | ^~~~~~~~~~~ bridge2.c:163:26: warning: unused variable ‘post_prec_eta’ [-Wunused-variable] 163 | double post_mean_eta=0,post_prec_eta=0; | ^~~~~~~~~~~~~ bridge2.c:163:10: warning: unused variable ‘post_mean_eta’ [-Wunused-variable] 163 | double post_mean_eta=0,post_prec_eta=0; | ^~~~~~~~~~~~~ bridge2.c:162:28: warning: unused variable ‘post_prec_delta’ [-Wunused-variable] 162 | double post_mean_delta=0,post_prec_delta=0; | ^~~~~~~~~~~~~~~ bridge2.c:162:10: warning: unused variable ‘post_mean_delta’ [-Wunused-variable] 162 | double post_mean_delta=0,post_prec_delta=0; | ^~~~~~~~~~~~~~~ bridge2.c:161:28: warning: unused variable ‘post_prec_alpha’ [-Wunused-variable] 161 | double post_mean_alpha=0,post_prec_alpha=0; | ^~~~~~~~~~~~~~~ bridge2.c:161:10: warning: unused variable ‘post_mean_alpha’ [-Wunused-variable] 161 | double post_mean_alpha=0,post_prec_alpha=0; | ^~~~~~~~~~~~~~~ bridge2.c:160:27: warning: unused variable ‘post_prec_beta’ [-Wunused-variable] 160 | double post_mean_beta=0,post_prec_beta=0; | ^~~~~~~~~~~~~~ bridge2.c:160:10: warning: unused variable ‘post_mean_beta’ [-Wunused-variable] 160 | double post_mean_beta=0,post_prec_beta=0; | ^~~~~~~~~~~~~~ bridge2.c:159:25: warning: unused variable ‘post_prec_mu’ [-Wunused-variable] 159 | double post_mean_mu=0,post_prec_mu=0; | ^~~~~~~~~~~~ bridge2.c:159:10: warning: unused variable ‘post_mean_mu’ [-Wunused-variable] 159 | double post_mean_mu=0,post_prec_mu=0; | ^~~~~~~~~~~~ bridge2.c:154:19: warning: unused variable ‘dens_t_new’ [-Wunused-variable] 154 | double dens_t=0,dens_t_new=0; | ^~~~~~~~~~ bridge2.c:154:10: warning: unused variable ‘dens_t’ [-Wunused-variable] 154 | double dens_t=0,dens_t_new=0; | ^~~~~~ bridge2.c:150:21: warning: variable ‘SSgammasd’ set but not used [-Wunused-but-set-variable] 150 | double SSgamma=0, SSgammasd=0; | ^~~~~~~~~ bridge2.c:150:10: warning: variable ‘SSgamma’ set but not used [-Wunused-but-set-variable] 150 | double SSgamma=0, SSgammasd=0; | ^~~~~~~ bridge2.c:145:10: warning: unused variable ‘pi’ [-Wunused-variable] 145 | double pi=3.14; | ^~ bridge2.c:143:19: warning: unused variable ‘dens_rho_new’ [-Wunused-variable] 143 | double dens_rho,dens_rho_new; | ^~~~~~~~~~~~ bridge2.c:143:10: warning: unused variable ‘dens_rho’ [-Wunused-variable] 143 | double dens_rho,dens_rho_new; | ^~~~~~~~ bridge2.c:142:20: warning: unused variable ‘sum_rho_new’ [-Wunused-variable] 142 | double sum_rho=0,sum_rho_new=0; | ^~~~~~~~~~~ bridge2.c:142:10: warning: unused variable ‘sum_rho’ [-Wunused-variable] 142 | double sum_rho=0,sum_rho_new=0; | ^~~~~~~ bridge2.c:138:10: warning: unused variable ‘rho_new’ [-Wunused-variable] 138 | double rho_new; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bridge2_util.c -o bridge2_util.o In file included from /home/biocbuild/bbs-3.14-bioc/R/include/R.h:80, from bridge2_util.h:1, from bridge2_util.c:1: bridge2_util.c: In function ‘qr_solve’: bridge2_util.c:570:14: warning: implicit declaration of function ‘dqrdc2_’ [-Wimplicit-function-declaration] 570 | F77_CALL(dqrdc2)(xt, &n, &n, &p, &tol, &rank,qraux, pivot, work); | ^~~~~~ /home/biocbuild/bbs-3.14-bioc/R/include/R_ext/RS.h:92:22: note: in definition of macro ‘F77_CALL’ 92 | # define F77_CALL(x) x ## _ | ^ bridge2_util.c:585:14: warning: implicit declaration of function ‘dqrcf_’ [-Wimplicit-function-declaration] 585 | F77_CALL(dqrcf)(xt, &n, &rank, qraux,yt, &n, coeft, &info); | ^~~~~ /home/biocbuild/bbs-3.14-bioc/R/include/R_ext/RS.h:92:22: note: in definition of macro ‘F77_CALL’ 92 | # define F77_CALL(x) x ## _ | ^ bridge2_util.c:549:11: warning: unused variable ‘vmax’ [-Wunused-variable] 549 | char *vmax; | ^~~~ bridge2_util.c: In function ‘inverse’: bridge2_util.c:608:9: warning: unused variable ‘j’ [-Wunused-variable] 608 | int i,j; | ^ bridge2_util.c: In function ‘product_mat_vec’: bridge2_util.c:655:11: warning: unused variable ‘k’ [-Wunused-variable] 655 | int i,j,k; | ^ bridge2_util.c: In function ‘slice_sampling_b’: bridge2_util.c:763:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 763 | while(J>0 & z0 & z0 & z0 & z0 & z0 & z0 & z0 & z