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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CBN2Path.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CBN2Path_0.99.17.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CBN2Path.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* this is package ‘CBN2Path’ version ‘0.99.17’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CBN2Path’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* checking code 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bcbn: no visible global function definition for ‘SnowParam’
bcbn: no visible binding for global variable ‘datasets’
ctcbn: no visible global function definition for ‘SnowParam’
generateGeomNodePoint: no visible binding for global variable ‘nodes’
generateGeomNodeText: no visible binding for global variable ‘nodes’
generateGgText: no visible binding for global variable ‘x’
generateGgText: no visible binding for global variable ‘y’
generateGgText: no visible binding for global variable ‘label’
generateMatrixGenotypes : f1 : <anonymous>: no visible global function
  definition for ‘combn’
hcbn: no visible global function definition for ‘SnowParam’
variableCapSize: no visible binding for global variable ‘edges’
variableCapSize: no visible binding for global variable ‘x’
variableCapSize: no visible binding for global variable ‘y’
visualizeCBNModel: no visible binding for global variable ‘name’
visualizeFitnessLandscape: no visible binding for global variable ‘x’
visualizeFitnessLandscape: no visible binding for global variable ‘y’
visualizeFitnessLandscape: no visible binding for global variable
  ‘name’
visualizeProbabilities: no visible binding for global variable ‘name’
Undefined global functions or variables:
  SnowParam combn datasets edges label name nodes x y
Consider adding
  importFrom("utils", "combn")
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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
hcbnSingle              73.309  0.367  73.679
pathProbQuartetBCBN     31.387  0.434  31.822
visualizeProbabilities  31.223  0.166  31.389
bcbn                    14.497  1.125  15.622
jensenShannonDivergence 10.233  0.558  10.791
Predictability           9.064  0.479   9.544
pathProbQuartetRCBN      7.792  0.304   8.096
pathProbQuartetHCBN      6.278  0.234   6.513
pathProbQuartetCTCBN     5.845  0.361   6.206
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CBN2Path.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CBN2Path
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CBN2Path’ ...
** this is package ‘CBN2Path’ version ‘0.99.17’
** using staged installation
checking for gcc... gcc -std=gnu2x
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
checking for gsl-config... /usr/bin/gsl-config
checking if GSL version >= 2.5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bcbn.c -o bcbn.o
bcbn.c: In function ‘bcbn_write_poset’:
bcbn.c:228:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  228 |     for (j=0; j<n; j++)
      |     ^~~
bcbn.c:232:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  232 |       fprintf(output, "0 0\n");
      |       ^~~~~~~
bcbn.c: In function ‘bcbn_is_equal_int_matrix’:
bcbn.c:332:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  332 |     for (j=0; j<n; j++)
      |     ^~~
bcbn.c:336:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  336 |       return 1;
      |       ^~~~~~
bcbn.c: In function ‘bcbn_free_lattice_children’:
bcbn.c:433:7: warning: unused variable ‘i’ [-Wunused-variable]
  433 |   int i;
      |       ^
bcbn.c: In function ‘bcbn_print_genotype’:
bcbn.c:641:7: warning: unused variable ‘i’ [-Wunused-variable]
  641 |   int i;
      |       ^
bcbn.c: In function ‘bcbn_bfs_order_ideals’:
bcbn.c:691:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  691 |         for (j=0; j<lin_ext_size; j++)
      |         ^~~
bcbn.c:697:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  697 |           if (! is_in)  // add to linear extension:
      |           ^~
bcbn.c: In function ‘bcbn_hamming_distance’:
bcbn.c:794:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  794 |   for(i=0; i<n; i++)
      |   ^~~
bcbn.c:801:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  801 |     free(g);
      |     ^~~~
bcbn.c: In function ‘compute_all_cbn_prob’:
bcbn.c:1056:13: warning: unused variable ‘k’ [-Wunused-variable]
 1056 |   int i,j,c,k;
      |             ^
bcbn.c:1056:9: warning: unused variable ‘j’ [-Wunused-variable]
 1056 |   int i,j,c,k;
      |         ^
bcbn.c: In function ‘bcbn_reduce_to_cover_relations’:
bcbn.c:1212:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1212 |     for (j=0; j<n; j++)
      |     ^~~
bcbn.c:1219:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1219 |       while (empty(&q) == FALSE)
      |       ^~~~~
bcbn.c: In function ‘compute_likelihood’:
bcbn.c:1281:15: warning: unused variable ‘likelihood’ [-Wunused-variable]
 1281 |   long double likelihood, likelihood_d;
      |               ^~~~~~~~~~
bcbn.c: In function ‘relocate_theta_i’:
bcbn.c:1367:25: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
 1367 |   double alpha,beta,var,x;
      |                         ^
bcbn.c:1367:21: warning: unused variable ‘var’ [-Wunused-variable]
 1367 |   double alpha,beta,var,x;
      |                     ^~~
bcbn.c: In function ‘compute_theta_transition_prob’:
bcbn.c:1380:25: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
 1380 |   double alpha,beta,var,x;
      |                         ^
bcbn.c:1380:21: warning: unused variable ‘var’ [-Wunused-variable]
 1380 |   double alpha,beta,var,x;
      |                     ^~~
bcbn.c: In function ‘propose_new_cover_relation’:
bcbn.c:1449:11: warning: unused variable ‘k’ [-Wunused-variable]
 1449 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘get_tp_for_new_cover_move’:
bcbn.c:1550:35: warning: unused variable ‘k’ [-Wunused-variable]
 1550 |   int i,j,N_all_comp,N_compatible,k;
      |                                   ^
bcbn.c:1550:22: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1550 |   int i,j,N_all_comp,N_compatible,k;
      |                      ^~~~~~~~~~~~
bcbn.c:1550:11: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1550 |   int i,j,N_all_comp,N_compatible,k;
      |           ^~~~~~~~~~
bcbn.c: In function ‘relocate_epsilon’:
bcbn.c:1675:25: warning: unused variable ‘x’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |                         ^
bcbn.c:1675:21: warning: unused variable ‘var’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |                     ^~~
bcbn.c:1675:16: warning: unused variable ‘beta’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |                ^~~~
bcbn.c:1675:10: warning: unused variable ‘alpha’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |          ^~~~~
bcbn.c: In function ‘propose_new_bcbn_transitive_closure_relation’:
bcbn.c:1755:11: warning: unused variable ‘k’ [-Wunused-variable]
 1755 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘propose_delete_bcbn_transitive_closure_relation’:
bcbn.c:1878:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1878 |   int i,j,k,N_compatible,N_all_comp;
      |                          ^~~~~~~~~~
bcbn.c:1878:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1878 |   int i,j,k,N_compatible,N_all_comp;
      |             ^~~~~~~~~~~~
bcbn.c:1878:11: warning: unused variable ‘k’ [-Wunused-variable]
 1878 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘get_tp_for_delete_bcbn_transitive_closure_relation_move’:
bcbn.c:1957:7: warning: unused variable ‘c’ [-Wunused-variable]
 1957 |   int c = 0;
      |       ^
bcbn.c:1946:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1946 |   int i,j,k,N_compatible,N_all_comp;
      |                          ^~~~~~~~~~
bcbn.c:1946:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1946 |   int i,j,k,N_compatible,N_all_comp;
      |             ^~~~~~~~~~~~
bcbn.c:1946:11: warning: unused variable ‘k’ [-Wunused-variable]
 1946 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘get_tp_for_new_bcbn_transitive_closure_relation_move’:
bcbn.c:2008:7: warning: unused variable ‘c’ [-Wunused-variable]
 2008 |   int c = 0;
      |       ^
bcbn.c:1997:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1997 |   int i,j,k,N_compatible,N_all_comp;
      |                          ^~~~~~~~~~
bcbn.c:1997:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1997 |   int i,j,k,N_compatible,N_all_comp;
      |             ^~~~~~~~~~~~
bcbn.c:1997:11: warning: unused variable ‘k’ [-Wunused-variable]
 1997 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘start_Exp_theta_MH’:
bcbn.c:2362:7: warning: unused variable ‘accepted’ [-Wunused-variable]
 2362 |   int accepted = 0;
      |       ^~~~~~~~
bcbn.c:2358:9: warning: unused variable ‘j’ [-Wunused-variable]
 2358 |   int i,j,k = 0;
      |         ^
bcbn.c:2358:7: warning: unused variable ‘i’ [-Wunused-variable]
 2358 |   int i,j,k = 0;
      |       ^
bcbn.c: In function ‘run_MH_sampler’:
bcbn.c:2620:22: warning: unused variable ‘MH_ratio’ [-Wunused-variable]
 2620 |   long double alpha, MH_ratio;
      |                      ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ctcbn.c -o ctcbn.o
In file included from ctcbn.c:3:
ct-cbn.h: In function ‘print_int_array’:
ct-cbn.h:184:7: warning: unused variable ‘j’ [-Wunused-variable]
  184 |   int j;
      |       ^
ct-cbn.h: In function ‘write_poset’:
ct-cbn.h:274:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  274 |     for (j=1; j<=n; j++)
      |     ^~~
ct-cbn.h:278:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  278 |       fprintf(output, "0\n");
      |       ^~~~~~~
ct-cbn.h: In function ‘print_genotype’:
ct-cbn.h:803:7: warning: unused variable ‘i’ [-Wunused-variable]
  803 |   int i;
      |       ^
ct-cbn.h: In function ‘bfs_order_ideals’:
ct-cbn.h:853:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  853 |         for (j=0; j<lin_ext_size; j++)
      |         ^~~
ct-cbn.h:859:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  859 |           if (! is_in)  // add to linear extension:
      |           ^~
ct-cbn.h: In function ‘hamming_distance’:
ct-cbn.h:956:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  956 |   for(i=0; i<n; i++)
      |   ^~~
ct-cbn.h:963:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  963 |     free(g);
      |     ^~~~
ct-cbn.h: In function ‘is_after’:
ct-cbn.h:1198:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1198 |     for ( a=0; a<=M->n; a++ )
      |     ^~~
ct-cbn.h:1201:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1201 |       return 1;
      |       ^~~~~~
ct-cbn.h: In function ‘is_strict_after’:
ct-cbn.h:1211:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1211 |     for ( a=0; a<=M->n; a++ )
      |     ^~~
ct-cbn.h:1214:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1214 |       return 1;
      |       ^~~~~~
ct-cbn.h: In function ‘compute_all_exp’:
ct-cbn.h:1283: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1283 | #pragma omp parallel for private(i,c,k,j,g, all_pred_in_k, pred,l)
      | 
ct-cbn.h:1318:11: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1318 |           for (l = 0; l < m; l++)
      |           ^~~
ct-cbn.h:1346:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1346 |             Exp[pos][i] = censexp[pos][i][m-1];
      |             ^~~
ct-cbn.h: In function ‘EM_epsilon’:
ct-cbn.h:1440:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1440 |       for(i = 1; i < m; i++)
      |       ^~~
ct-cbn.h:1447:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1447 |         loglik_new += log (prob_tmp) * D[k].count;
      |         ^~~~~~~~~~
ct-cbn.h: In function ‘compute_loglik’:
ct-cbn.h:1471:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1471 |     for(i = 1; i < m; i++)
      |     ^~~
ct-cbn.h:1477:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1477 |       loglik[k] = log (prob_tmp) ;
      |       ^~~~~~
ct-cbn.h: In function ‘MLE’:
ct-cbn.h:1833:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1833 |     for (k=0; k<N_u; k++)
      |     ^~~
ct-cbn.h:1839:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1839 |       lambda[i] = (double) N / sum;
      |       ^~~~~~
ct-cbn.h: In function ‘EM’:
ct-cbn.h:1920:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1920 |     for (k=0; k<N_u; k++)
      |     ^~~
ct-cbn.h:1939:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1939 |       if (verbose)
      |       ^~
ct-cbn.h: In function ‘violation_map’:
ct-cbn.h:2488:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2488 |   for (i=1; i<=n; i++)
      |   ^~~
ct-cbn.h:2502:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2502 |     qsort(V, idx, sizeof(int *), compare_violation_pairs);  // small violators first
      |     ^~~~~
ct-cbn.h: In function ‘reduce_to_cover_relations’:
ct-cbn.h:2524:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2524 |     for (j=1; j<=n; j++)
      |     ^~~
ct-cbn.h:2531:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2531 |       while (empty(&q) == FALSE)
      |       ^~~~~
ct-cbn.h: In function ‘try_edge’:
ct-cbn.h:2741:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2741 |     for(j=0;j<n*n;j++)
      |     ^~~
ct-cbn.h:2744:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2744 |       R4[i] = c;
      |       ^~
ct-cbn.h:2784:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2784 |             for(i=1;i<n+1;i++)
      |             ^~~
ct-cbn.h:2790:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2790 |               if(c == 1)
      |               ^~
ct-cbn.h:2943:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2943 |             for(i=1;i<n+1;i++)
      |             ^~~
ct-cbn.h:2949:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2949 |               if(c == 1)
      |               ^~
ct-cbn.h:2721:17: warning: variable ‘alpha_new’ set but not used [-Wunused-but-set-variable]
 2721 |   double alpha, alpha_new;
      |                 ^~~~~~~~~
ct-cbn.h: In function ‘local_search’:
ct-cbn.h:3134:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 3134 |     for(j=1;j<=M->n;j++)
      |     ^~~
ct-cbn.h:3161:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 3161 |       print_double_matrix(loglik_next, M->n, M->n);
      |       ^~~~~~~~~~~~~~~~~~~
ct-cbn.h: In function ‘is_equal_int_matrix’:
ct-cbn.h:3196:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 3196 |     for (j=0; j<n; j++)
      |     ^~~
ct-cbn.h:3200:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 3200 |       return 1;
      |       ^~~~~~
ct-cbn.h: In function ‘ML_path’:
ct-cbn.h:3305:7: warning: variable ‘mut_next’ set but not used [-Wunused-but-set-variable]
 3305 |   int mut_next, index_next;
      |       ^~~~~~~~
ctcbn.c: In function ‘ctcbn_’:
ctcbn.c:88:7: warning: unused variable ‘c’ [-Wunused-variable]
   88 |   int c = 0;
      |       ^
ctcbn.c:84:7: warning: unused variable ‘GPS’ [-Wunused-variable]
   84 |   int GPS = 0;
      |       ^~~
ctcbn.c:79:7: warning: unused variable ‘verbose’ [-Wunused-variable]
   79 |   int verbose = 0;
      |       ^~~~~~~
ctcbn.c: In function ‘hcbn_’:
ctcbn.c:319:7: warning: unused variable ‘c’ [-Wunused-variable]
  319 |   int c = 0;
      |       ^
ctcbn.c:314:7: warning: variable ‘N_iter’ set but not used [-Wunused-but-set-variable]
  314 |   int N_iter = 0;
      |       ^~~~~~
ctcbn.c:313:10: warning: unused variable ‘T’ [-Wunused-variable]
  313 |   double T = REAL(temp)[0];
      |          ^
ctcbn.c:308:7: warning: unused variable ‘t_flag’ [-Wunused-variable]
  308 |   int t_flag = 1;
      |       ^~~~~~
ctcbn.c:306:7: warning: unused variable ‘l_flag’ [-Wunused-variable]
  306 |   int l_flag = 0;
      |       ^~~~~~
ctcbn.c:305:7: warning: unused variable ‘gps_flag’ [-Wunused-variable]
  305 |   int gps_flag = 0;
      |       ^~~~~~~~
ctcbn.c:304:7: warning: variable ‘e_flag’ set but not used [-Wunused-but-set-variable]
  304 |   int e_flag = 0;
      |       ^~~~~~
ctcbn.c:303:7: warning: unused variable ‘f_flag’ [-Wunused-variable]
  303 |   int f_flag = 0;
      |       ^~~~~~
ctcbn.c:302:7: warning: unused variable ‘error_flag’ [-Wunused-variable]
  302 |   int error_flag = 0;
      |       ^~~~~~~~~~
ctcbn.c:468:10: warning: ‘rOutput’ may be used uninitialized [-Wmaybe-uninitialized]
  468 |   return char_to_sexp(rOutput);
      |          ^~~~~~~~~~~~~~~~~~~~~
ctcbn.c:320:9: note: ‘rOutput’ was declared here
  320 |   char* rOutput;
      |         ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c queue.c -o queue.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o CBN2Path.so bcbn.o ctcbn.o init.o queue.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-CBN2Path/00new/CBN2Path/libs
** R
** 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 (CBN2Path)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(CBN2Path)
> 
> test_check("CBN2Path")
chain: 1
0
chain: 2
0
chain: 3
0
chain: 4
0
       V1               V2               V3                V4         
 Min.   :0.2608   Min.   :0.1346   Min.   :0.03498   Min.   :0.01468  
 1st Qu.:0.8184   1st Qu.:0.7293   1st Qu.:0.62820   1st Qu.:0.08346  
 Median :0.9047   Median :0.8363   Median :0.75826   Median :0.10632  
 Mean   :0.8748   Mean   :0.8102   Mean   :0.73571   Mean   :0.11062  
 3rd Qu.:0.9580   3rd Qu.:0.9199   3rd Qu.:0.86664   3rd Qu.:0.13431  
 Max.   :1.0000   Max.   :1.0000   Max.   :0.99998   Max.   :0.33475  
       V5         
 Min.   :-10.932  
 1st Qu.: -6.601  
 Median : -6.159  
 Mean   : -6.283  
 3rd Qu.: -5.838  
 Max.   : -5.302  
       V1               V2                V3               V4         
 Min.   :0.2870   Min.   :0.05837   Min.   :0.0471   Min.   :0.01391  
 1st Qu.:0.8228   1st Qu.:0.72244   1st Qu.:0.6238   1st Qu.:0.08473  
 Median :0.9067   Median :0.83328   Median :0.7534   Median :0.10939  
 Mean   :0.8777   Mean   :0.80710   Mean   :0.7316   Mean   :0.11282  
 3rd Qu.:0.9616   3rd Qu.:0.91788   3rd Qu.:0.8608   3rd Qu.:0.13578  
 Max.   :0.9999   Max.   :0.99986   Max.   :0.9999   Max.   :0.28584  
       V5         
 Min.   :-12.669  
 1st Qu.: -6.593  
 Median : -6.157  
 Mean   : -6.281  
 3rd Qu.: -5.832  
 Max.   : -5.306  
       V1               V2               V3                V4         
 Min.   :0.1706   Min.   :0.1149   Min.   :0.02682   Min.   :0.01372  
 1st Qu.:0.8222   1st Qu.:0.7258   1st Qu.:0.62805   1st Qu.:0.08601  
 Median :0.9058   Median :0.8356   Median :0.76235   Median :0.11018  
 Mean   :0.8761   Mean   :0.8077   Mean   :0.73759   Mean   :0.11248  
 3rd Qu.:0.9595   3rd Qu.:0.9175   3rd Qu.:0.86851   3rd Qu.:0.13500  
 Max.   :1.0000   Max.   :1.0000   Max.   :0.99994   Max.   :0.29070  
       V5         
 Min.   :-10.800  
 1st Qu.: -6.564  
 Median : -6.139  
 Mean   : -6.258  
 3rd Qu.: -5.814  
 Max.   : -5.309  
       V1               V2                V3                V4         
 Min.   :0.2657   Min.   :0.08261   Min.   :0.05012   Min.   :0.01477  
 1st Qu.:0.8237   1st Qu.:0.72570   1st Qu.:0.62530   1st Qu.:0.08379  
 Median :0.9060   Median :0.83719   Median :0.75755   Median :0.10779  
 Mean   :0.8751   Mean   :0.80834   Mean   :0.73520   Mean   :0.11176  
 3rd Qu.:0.9589   3rd Qu.:0.91974   3rd Qu.:0.86877   3rd Qu.:0.13649  
 Max.   :1.0000   Max.   :0.99997   Max.   :0.99999   Max.   :0.29176  
       V5         
 Min.   :-11.164  
 1st Qu.: -6.589  
 Median : -6.157  
 Mean   : -6.279  
 3rd Qu.: -5.830  
 Max.   : -5.318  
[1] "Criterion: 1.00110820782812"
Potential scale reduction factors:

     Point est. Upper C.I.
[1,]          1          1
[2,]          1          1
[3,]          1          1
[4,]          1          1
[5,]          1          1

Multivariate psrf

1
[1] "##########################################"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 9 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 98.727   1.121  99.839