bridge 1.46.0
Raphael Gottardo
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/bridge |
| Branch: RELEASE_3_8 |
| Last Commit: 558dd74 |
| Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | [ OK ] | OK | WARNINGS | |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL bridge
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘bridge’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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]
int count_model=0;
^
bridge2.affy.c:36:7: warning: unused variable ‘old_model’ [-Wunused-variable]
int old_model;
^
bridge2.affy.c: In function ‘up_date_w2’:
bridge2.affy.c:302:3: warning: implicit declaration of function ‘dirichlet’ [-Wimplicit-function-declaration]
dirichlet(gamma, 2, w);
^
bridge2.affy.c:282:10: warning: unused variable ‘w_new’ [-Wunused-variable]
double w_new[2];
^
gcc -I"/home/biocbuild/bbs-3.8-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]
double old_a=0,width_a=5;
^
bridge2.c:199:10: warning: unused variable ‘old_a’ [-Wunused-variable]
double old_a=0,width_a=5;
^
bridge2.c:198:18: warning: unused variable ‘width_b’ [-Wunused-variable]
double old_b=0,width_b=5;
^
bridge2.c:198:10: warning: unused variable ‘old_b’ [-Wunused-variable]
double old_b=0,width_b=5;
^
bridge2.c:192:10: warning: unused variable ‘sum_res2’ [-Wunused-variable]
double sum_res2;
^
bridge2.c:191:10: warning: unused variable ‘sum_res1’ [-Wunused-variable]
double sum_res1;
^
bridge2.c:177:7: warning: unused variable ‘countp’ [-Wunused-variable]
int countp=0;
^
bridge2.c:175:7: warning: unused variable ‘countb_eps’ [-Wunused-variable]
int countb_eps=0;
^
bridge2.c:174:7: warning: unused variable ‘counta_eps’ [-Wunused-variable]
int counta_eps=0;
^
bridge2.c:173:7: warning: unused variable ‘counta’ [-Wunused-variable]
int counta=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: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:164:24: warning: variable ‘mean_gamma2’ set but not used [-Wunused-but-set-variable]
double mean_gamma1=0,mean_gamma2=0;
^
bridge2.c:164:10: warning: variable ‘mean_gamma1’ set but not used [-Wunused-but-set-variable]
double mean_gamma1=0,mean_gamma2=0;
^
bridge2.c:163:26: warning: unused variable ‘post_prec_eta’ [-Wunused-variable]
double post_mean_eta=0,post_prec_eta=0;
^
bridge2.c:163:10: warning: unused variable ‘post_mean_eta’ [-Wunused-variable]
double post_mean_eta=0,post_prec_eta=0;
^
bridge2.c:162:28: warning: unused variable ‘post_prec_delta’ [-Wunused-variable]
double post_mean_delta=0,post_prec_delta=0;
^
bridge2.c:162:10: warning: unused variable ‘post_mean_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:161:10: warning: unused variable ‘post_mean_alpha’ [-Wunused-variable]
double post_mean_alpha=0,post_prec_alpha=0;
^
bridge2.c:160:27: warning: unused variable ‘post_prec_beta’ [-Wunused-variable]
double post_mean_beta=0,post_prec_beta=0;
^
bridge2.c:160:10: warning: unused variable ‘post_mean_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:159:10: warning: unused variable ‘post_mean_mu’ [-Wunused-variable]
double post_mean_mu=0,post_prec_mu=0;
^
bridge2.c:154:19: warning: unused variable ‘dens_t_new’ [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
bridge2.c:154:10: warning: unused variable ‘dens_t’ [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
bridge2.c:150:21: warning: variable ‘SSgammasd’ set but not used [-Wunused-but-set-variable]
double SSgamma=0, SSgammasd=0;
^
bridge2.c:150:10: warning: variable ‘SSgamma’ set but not used [-Wunused-but-set-variable]
double SSgamma=0, SSgammasd=0;
^
bridge2.c:145:10: warning: unused variable ‘pi’ [-Wunused-variable]
double pi=3.14;
^
bridge2.c:143:19: warning: unused variable ‘dens_rho_new’ [-Wunused-variable]
double dens_rho,dens_rho_new;
^
bridge2.c:143:10: warning: unused variable ‘dens_rho’ [-Wunused-variable]
double dens_rho,dens_rho_new;
^
bridge2.c:142:20: warning: unused variable ‘sum_rho_new’ [-Wunused-variable]
double sum_rho=0,sum_rho_new=0;
^
bridge2.c:142:10: warning: unused variable ‘sum_rho’ [-Wunused-variable]
double sum_rho=0,sum_rho_new=0;
^
bridge2.c:138:10: warning: unused variable ‘rho_new’ [-Wunused-variable]
double rho_new;
^
gcc -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/R.h:91:0,
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]
F77_CALL(dqrdc2)(xt, &n, &n, &p, &tol, &rank,qraux, pivot, work);
^
/home/biocbuild/bbs-3.8-bioc/R/include/R_ext/RS.h:92:22: note: in definition of macro ‘F77_CALL’
# define F77_CALL(x) x ## _
^
bridge2_util.c:585:14: warning: implicit declaration of function ‘dqrcf_’ [-Wimplicit-function-declaration]
F77_CALL(dqrcf)(xt, &n, &rank, qraux,yt, &n, coeft, &info);
^
/home/biocbuild/bbs-3.8-bioc/R/include/R_ext/RS.h:92:22: note: in definition of macro ‘F77_CALL’
# define F77_CALL(x) x ## _
^
bridge2_util.c:549:11: warning: unused variable ‘vmax’ [-Wunused-variable]
char *vmax;
^
bridge2_util.c: In function ‘inverse’:
bridge2_util.c:608:9: warning: unused variable ‘j’ [-Wunused-variable]
int i,j;
^
bridge2_util.c: In function ‘product_mat_vec’:
bridge2_util.c:655:11: warning: unused variable ‘k’ [-Wunused-variable]
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]
while(J>0 & z<log_f_L)
^
bridge2_util.c:771:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
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]
while(J>0 & z<log_f_L)
^
bridge2_util.c:826:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
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]
while(J>0 & z<log_f_L)
^
bridge2_util.c:884:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
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]
while(J>0 & z<log_f_L)
^
bridge2_util.c:969:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
while(K>0 & z<log_f_R)
^
gcc -I"/home/biocbuild/bbs-3.8-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]
int count_model=0;
^
bridge3.c:37:7: warning: unused variable ‘old_model’ [-Wunused-variable]
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]
int old_model;
^
bridge3.c: In function ‘gibbs_mu’:
bridge3.c:332:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
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]
double w_new[5];
^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/bridge/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bridge)