##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL bridge
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘bridge’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-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-3.16-bioc/R/include/R_ext/RS.h:77:22: note: in definition of macro ‘F77_CALL’
77 | # 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-3.16-bioc/R/include/R_ext/RS.h:77:22: note: in definition of macro ‘F77_CALL’
77 | # 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 & z<log_f_L)
| ~^~
bridge2_util.c:771:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
771 | while(K>0 & z<log_f_R)
| ~^~
bridge2_util.c: In function ‘slice_sampling_a’:
bridge2_util.c:818:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
818 | while(J>0 & z<log_f_L)
| ~^~
bridge2_util.c:826:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
826 | while(K>0 & z<log_f_R)
| ~^~
bridge2_util.c: In function ‘slice_sampling_rho’:
bridge2_util.c:875:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
875 | while(J>0 & z<log_f_L)
| ~^~
bridge2_util.c:884:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
884 | while(K>0 & z<log_f_R)
| ~^~
bridge2_util.c: In function ‘slice_sampling_p’:
bridge2_util.c:961:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
961 | while(J>0 & z<log_f_L)
| ~^~
bridge2_util.c:969:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
969 | while(K>0 & z<log_f_R)
| ~^~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bridge3.c -o bridge3.o
bridge3.c: In function ‘gene_express_3s’:
bridge3.c:38:7: warning: unused variable ‘count_model’ [-Wunused-variable]
38 | int count_model=0;
| ^~~~~~~~~~~
bridge3.c:37:7: warning: unused variable ‘old_model’ [-Wunused-variable]
37 | int old_model;
| ^~~~~~~~~
bridge3.c: In function ‘all_gibbs’:
bridge3.c:190:7: warning: variable ‘old_model’ set but not used [-Wunused-but-set-variable]
190 | int old_model;
| ^~~~~~~~~
bridge3.c: In function ‘gibbs_mu’:
bridge3.c:332:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
332 | else if((w_star[3]<u) & u<w_star[4])
| ~^~~~~~~~~~
bridge3.c: In function ‘up_date_w’:
bridge3.c:362:10: warning: unused variable ‘w_new’ [-Wunused-variable]
362 | double w_new[5];
| ^~~~~
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-bridge/00new/bridge/libs
** R
** data
** byte-compile and prepare package for lazy loading
Warning message:
Package 'rama' is deprecated and will be removed from Bioconductor
version 3.17
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'rama' is deprecated and will be removed from Bioconductor
version 3.17
Warning: Package 'bridge' is deprecated and will be removed from Bioconductor
version 3.17
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'rama' is deprecated and will be removed from Bioconductor
version 3.17
Warning: Package 'bridge' is deprecated and will be removed from Bioconductor
version 3.17
** testing if installed package keeps a record of temporary installation path
* DONE (bridge)
