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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_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CBN2Path.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.0.0’
* 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              72.813  0.054  72.869
visualizeProbabilities  33.855  0.275  34.131
pathProbQuartetBCBN     30.696  0.366  31.062
bcbn                    14.239  1.127  15.366
jensenShannonDivergence  8.528  0.443   8.972
Predictability           7.333  0.319   7.651
pathProbQuartetRCBN      6.895  0.257   7.153
pathProbQuartetHCBN      5.266  0.242   5.508
pathProbQuartetCTCBN     5.093  0.300   5.393
* 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 ‘1.0.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.   :0.2211   Min.   :7.391e-05   Min.   :3.567e-05   Min.   :0.01083  
 1st Qu.:0.8223   1st Qu.:2.942e-01   1st Qu.:3.901e-01   1st Qu.:0.08617  
 Median :0.9040   Median :4.397e-01   Median :5.253e-01   Median :0.11271  
 Mean   :0.8764   Mean   :4.511e-01   Mean   :5.271e-01   Mean   :0.11719  
 3rd Qu.:0.9595   3rd Qu.:5.934e-01   3rd Qu.:6.622e-01   3rd Qu.:0.14409  
 Max.   :1.0000   Max.   :9.986e-01   Max.   :9.998e-01   Max.   :0.31728  
       V5         
 Min.   :-12.586  
 1st Qu.: -7.768  
 Median : -7.350  
 Mean   : -7.453  
 3rd Qu.: -7.019  
 Max.   : -6.507  
       V1               V2                  V3                  V4         
 Min.   :0.2433   Min.   :0.0002862   Min.   :2.573e-05   Min.   :0.01738  
 1st Qu.:0.8206   1st Qu.:0.2904598   1st Qu.:3.889e-01   1st Qu.:0.08657  
 Median :0.9040   Median :0.4369557   Median :5.288e-01   Median :0.11281  
 Mean   :0.8754   Mean   :0.4492621   Mean   :5.265e-01   Mean   :0.11692  
 3rd Qu.:0.9579   3rd Qu.:0.5945650   3rd Qu.:6.639e-01   3rd Qu.:0.14469  
 Max.   :1.0000   Max.   :0.9999815   Max.   :9.986e-01   Max.   :0.30248  
       V5         
 Min.   :-11.942  
 1st Qu.: -7.744  
 Median : -7.337  
 Mean   : -7.448  
 3rd Qu.: -7.025  
 Max.   : -6.506  
       V1               V2                  V3                 V4         
 Min.   :0.2194   Min.   :8.740e-06   Min.   :0.000817   Min.   :0.01781  
 1st Qu.:0.8189   1st Qu.:2.949e-01   1st Qu.:0.388975   1st Qu.:0.08574  
 Median :0.9036   Median :4.365e-01   Median :0.523449   Median :0.11267  
 Mean   :0.8745   Mean   :4.517e-01   Mean   :0.526054   Mean   :0.11645  
 3rd Qu.:0.9576   3rd Qu.:5.980e-01   3rd Qu.:0.666215   3rd Qu.:0.14368  
 Max.   :1.0000   Max.   :9.999e-01   Max.   :0.999832   Max.   :0.33464  
       V5         
 Min.   :-11.366  
 1st Qu.: -7.759  
 Median : -7.347  
 Mean   : -7.453  
 3rd Qu.: -7.034  
 Max.   : -6.508  
       V1               V2                  V3                 V4         
 Min.   :0.2514   Min.   :0.0003005   Min.   :0.001218   Min.   :0.01623  
 1st Qu.:0.8219   1st Qu.:0.2941134   1st Qu.:0.388829   1st Qu.:0.08697  
 Median :0.9032   Median :0.4382574   Median :0.523764   Median :0.11379  
 Mean   :0.8745   Mean   :0.4496047   Mean   :0.524743   Mean   :0.11703  
 3rd Qu.:0.9573   3rd Qu.:0.5941168   3rd Qu.:0.662525   3rd Qu.:0.14307  
 Max.   :1.0000   Max.   :0.9997472   Max.   :0.999789   Max.   :0.33910  
       V5         
 Min.   :-12.457  
 1st Qu.: -7.741  
 Median : -7.336  
 Mean   : -7.437  
 3rd Qu.: -7.020  
 Max.   : -6.512  
[1] "Criterion: 1.0008149795584"
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 
100.512   0.980 101.481