##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:bridge.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings bridge_1.62.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/bridge.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘bridge/DESCRIPTION’ ... OK
* this is package ‘bridge’ version ‘1.62.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bridge’ can be installed ... WARNING
Found the following significant warnings:
  bridge2.affy.c:302:3: warning: implicit declaration of function ‘dirichlet’; did you mean ‘dirichlet2’? [-Wimplicit-function-declaration]
  bridge2_util.c:570:14: warning: implicit declaration of function ‘dqrdc2_’ [-Wimplicit-function-declaration]
  bridge2_util.c:585:14: warning: implicit declaration of function ‘dqrcf_’ [-Wimplicit-function-declaration]
  bridge2_util.c:763:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:771:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:818:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:826:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:875:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:884:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:961:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge2_util.c:969:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  bridge3.c:332:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Warning: Package 'rama' is deprecated and will be removed from Bioconductor
  Warning: Package 'bridge' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.16-bioc/meat/bridge.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: Package 'rama' is deprecated and will be removed from Bioconductor
  version 3.17

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rama’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘rama’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘bridge/R/zzz.R’:
  .onLoad calls:
    require("rama", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

bridge.2samples: no visible global function definition for ‘var’
bridge.2samples: no visible global function definition for ‘median’
bridge.2samples: no visible global function definition for ‘mad’
bridge.3samples: no visible global function definition for ‘median’
bridge.3samples: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median var
Consider adding
  importFrom("stats", "mad", "median", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/bridge/libs/bridge.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bridge.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/bridge.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL bridge
###
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* 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)